GO:0055131 C3HC4-type RING finger domain binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0055131 defines the molecular function of binding to a C3HC4-type RING finger domain, a cysteine-rich zinc-coordinating module of 40-60 residues that binds two zinc ions.
• C3HC4-type RING fingers are the hallmark of many RING E3 ubiquitin ligases, including TRIM21 and RNF151, which use this domain to recruit E2 enzymes and ubiquitinate substrates.
• Proteins that bind C3HC4 domains can act as substrates, adaptors, or regulators of RING E3 ligase complexes, as shown for dysbindin binding to RNF151.
• The C3HC4-type RING finger gene family is expanded in metazoans; genome-wide analysis in silkworm identified multiple C3HC4 genes with immune-responsive expression.
• C3HC4 domain binding is linked to NF-kB signaling, autophagy, and antiviral immunity through linear ubiquitination and LUBAC components.
• CRISPR knockout, point-mutation, knock-in, and overexpression models enable causal dissection of C3HC4 domain interactions in disease and immunity.
Description
GO:0055131, C3HC4-type RING finger domain binding, is a molecular function term that describes the selective interaction of a protein with a C3HC4-type zinc finger domain. The C3HC4-type RING finger is a variant of the RING finger, a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions and adopts the consensus sequence C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C, where X is any amino acid. Many proteins containing a C3HC4-type RING finger play a key role in the ubiquitination pathway, acting as E3 ubiquitin ligases that transfer ubiquitin from E2 conjugating enzymes to substrate proteins. This domain binding function is therefore central to post-translational control of protein stability, localization, and signaling. Researchers study GO:0055131 to understand how RING finger proteins recognize their partners, how mutations in the domain alter interaction specificity, and how these interactions contribute to immunity, autophagy, and disease. For example, the porcine TRIM21 RING-finger E3 ubiquitin ligase is essential for anti-PRRSV activity, and its C3HC4 domain mediates critical protein-protein contacts. Similarly, RNF151, a testis-specific RING finger protein, interacts with dysbindin through its RING domain, linking C3HC4 binding to cytoskeletal and vesicular trafficking processes. Genome-wide identification of C3HC4-type zinc finger genes in silkworm has further revealed their immunological expression patterns, underscoring the evolutionary conservation and functional diversity of this domain family. Because C3HC4 domain binding is a hub for ubiquitin signaling, it is a high-value target for CRISPR-based functional genomics and therapeutic intervention.
C3HC4-type RING finger domain binding At A Glance
| GO ID | GO:0055131 |
|---|---|
| GO term | C3HC4-type RING finger domain binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to a C3HC4-type zinc finger domain of a protein, a RING finger variant that coordinates two zinc ions and is common in ubiquitination pathway proteins. |
| Domain consensus | C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C, where X is any amino acid. |
| Domain length | 40 to 60 residues. |
| Metal coordination | Coordinates two zinc ions. |
| Pathway association | Many C3HC4-type RING finger proteins play a key role in the ubiquitination pathway. |
What Is GO:0055131?
C3HC4-type RING finger domain binding (GO:0055131) is the molecular function of selectively and non-covalently interacting with a C3HC4-type zinc finger domain of a protein. The C3HC4-type zinc finger is a variant of the RING finger, a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions and has the consensus sequence C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C, where X is any amino acid. Many proteins containing a C3HC4-type RING finger play a key role in the ubiquitination pathway. This binding function is typically mediated by a partner protein that recognizes the folded RING domain, often to regulate E3 ubiquitin ligase activity, substrate recruitment, or complex assembly.
Why Is C3HC4-type RING finger domain binding Important in Cell Biology?
GO:0055131 is important because C3HC4-type RING finger domains are among the most abundant zinc-binding modules in eukaryotic proteomes and are central to ubiquitin-dependent signaling. Proteins that bind these domains can control the activity, stability, and substrate specificity of RING E3 ubiquitin ligases, thereby influencing diverse processes such as antiviral immunity, autophagy, NF-kB activation, and testis-specific protein trafficking. Dysregulation of C3HC4 domain interactions has been linked to immune evasion by viruses and to altered cell survival under stress. Because the domain is structurally defined and genetically tractable, it is an attractive target for CRISPR screens and for engineering synthetic binders. Understanding GO:0055131 therefore provides a mechanistic entry point for therapeutic modulation of ubiquitination in cancer, infection, and inflammatory disease.
• C3HC4-type RING fingers coordinate two zinc ions and adopt a compact fold that is ideal for protein-protein recognition.
• Many C3HC4 domain-containing proteins are E3 ubiquitin ligases that regulate substrate ubiquitination.
• C3HC4 domain binding controls linear ubiquitination and NF-kB activation at damaged lysosomes.
• LUBAC and OTULIN regulate autophagy initiation and maturation via linear ubiquitination and stabilization of ATG13, a process dependent on RING domain interactions.
• TRIM21 RING-finger E3 ligase activity is essential for anti-PRRSV activity in porcine cells.
• RNF151 interacts with dysbindin through its RING domain, linking C3HC4 binding to testis-specific functions.
• The C3HC4-type zinc finger gene family is expanded in silkworm and shows immune-responsive expression.
• C3HC4 domain interactions are implicated in plant basal immunity through NUCLEOTIDE-BINDING 9 regulation.
• CRISPR knockout and point-mutation models can test the causal role of C3HC4 domain residues in disease.
• C3HC4 domain binding is a druggable interface for modulating ubiquitin signaling in cancer and infection.
What Happens During C3HC4-type RING finger domain binding?
Recognition of the C3HC4 fold
In simple terms: A partner protein recognizes the shape of the C3HC4 zinc finger domain.
C3HC4-type RING finger domains fold around two zinc ions, creating a compact scaffold with exposed hydrophobic and polar surfaces. Binding partners, which may be substrates, adaptors, or regulatory proteins, recognize this fold through complementary surfaces. The consensus sequence C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C defines the zinc-coordinating residues that stabilize the domain. This recognition step is the first event in GO:0055131 and determines downstream specificity.
Complex assembly and E3 ligase recruitment
In simple terms: Binding brings together proteins that build a ubiquitin-transfer machine.
Once a partner binds the C3HC4 domain, it can recruit E2 ubiquitin-conjugating enzymes or stabilize the E3 ligase complex. For example, the porcine TRIM21 RING-finger E3 ubiquitin ligase requires its RING domain for anti-PRRSV activity, indicating that domain binding is essential for assembling a functional antiviral complex. Similarly, RNF151 interacts with dysbindin through its RING domain, linking C3HC4 binding to a specific protein complex in testis.
Substrate ubiquitination and signaling
In simple terms: The assembled complex tags target proteins with ubiquitin, changing their fate.
C3HC4 domain binding often positions a substrate for ubiquitination. Linear ubiquitination at damaged lysosomes induces local NF-kB activation and controls cell survival, a process that depends on RING domain-containing complexes. LUBAC and OTULIN regulate autophagy initiation and maturation by mediating linear ubiquitination and stabilization of ATG13, further demonstrating how C3HC4 domain interactions translate into signaling outcomes.
Regulation and feedback
In simple terms: The binding event is tuned by other proteins and post-translational modifications.
C3HC4 domain binding is not constitutive; it can be regulated by phosphorylation, ubiquitination, or competing interactors. OTULIN, a deubiquitinase, opposes LUBAC-mediated linear ubiquitination and thereby modulates the consequences of C3HC4 domain binding in autophagy and NF-kB signaling. In plants, the IMMUNE-ASSOCIATED NUCLEOTIDE-BINDING 9 protein regulates basal immunity, illustrating that C3HC4-related functions are integrated into broader immune signaling networks.
Key Genes Involved in GO:0055131 C3HC4-type RING finger domain binding
The following genes and proteins are experimentally linked to C3HC4-type RING finger domain binding or contain C3HC4 domains that mediate such interactions.
| Gene | Major Role | Research Relevance |
|---|---|---|
| TRIM21 | RING-finger E3 ubiquitin ligase with C3HC4 domain; essential for anti-PRRSV activity | Antiviral immunity; RING domain binding assays |
| RNF151 | Testis-specific RING finger protein that interacts with dysbindin | Protein-protein interaction; testis biology |
| C-RZF | RING zinc finger gene expressed in chicken embryo cells | Early characterization of RING domain expression |
| LUBAC components (HOIP, HOIL-1, Sharpin) | Linear ubiquitin chain assembly complex containing RING domains | NF-kB activation and autophagy regulation |
| OTULIN | Deubiquitinase that removes linear ubiquitin chains | Opposes LUBAC; regulates autophagy and NF-kB |
| ATG13 | Autophagy initiation factor stabilized by linear ubiquitination | Autophagy regulation via C3HC4-related complexes |
| NUCLEOTIDE-BINDING 9 (Arabidopsis) | Regulator of basal immunity | Plant immune signaling |
| C3HC4-type zinc finger genes (Bombyx mori) | Family of C3HC4 domain proteins with immune-responsive expression | Genome-wide identification and immunological analysis |
| Dysbindin | Binding partner of RNF151 | Cytoskeletal and vesicular trafficking |
| E2 ubiquitin-conjugating enzymes | Accept ubiquitin from E1 and transfer to substrate with E3 | Core ubiquitination machinery recruited by RING domains |
| NF-kB pathway components | Transcription factors activated by linear ubiquitination | Cell survival and inflammation |
| PRRSV viral proteins | Targets of TRIM21-mediated antiviral activity | Viral infection models |
| Zinc ions | Structural cofactors coordinated by C3HC4 domain | Domain folding and stability |
| Ubiquitin | Modifier transferred to substrates by RING E3 ligases | Ubiquitination pathway |
| Proteasome subunits | Degrade ubiquitinated substrates | Downstream of C3HC4-mediated ubiquitination |
How Is C3HC4-type RING finger domain binding Regulated?
C3HC4-type RING finger domain binding is regulated at multiple levels. The availability of zinc ions influences domain folding and thus binding competence. Post-translational modifications of either the RING domain or its binding partner can alter affinity. In the LUBAC-OTULIN system, the deubiquitinase OTULIN removes linear ubiquitin chains and thereby modulates the signaling output of C3HC4 domain-containing complexes during autophagy and NF-kB activation. Linear ubiquitination at damaged lysosomes locally activates NF-kB and controls cell survival, showing that the consequences of C3HC4 domain binding are spatially and temporally restricted. In antiviral immunity, TRIM21 RING-finger E3 ligase activity is essential for anti-PRRSV activity, and its regulation likely involves interferon signaling and viral countermeasures. Plant basal immunity regulated by NUCLEOTIDE-BINDING 9 further illustrates that C3HC4-related functions are integrated into inducible defense networks.
C3HC4-type RING finger domain binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| TRIM21 | Antiviral immunity against PRRSV | Porcine cell lines with TRIM21 knockout or point mutation |
| LUBAC components | NF-kB activation and cell survival at damaged lysosomes | Knockout and knock-in cell models |
| OTULIN | Autophagy regulation and inflammatory signaling | OTULIN knockout and overexpression models |
| RNF151 | Testis-specific protein interactions | Testis cell lines and knockout mice |
| NUCLEOTIDE-BINDING 9 | Plant basal immunity | Arabidopsis knockout and overexpression lines |
C3HC4 domain binding in antiviral immunity and infection
The porcine TRIM21 RING-finger E3 ubiquitin ligase is essential for anti-PRRSV activity, and its C3HC4 domain mediates critical interactions for viral restriction. This positions C3HC4 domain binding as a determinant of host susceptibility to viral infection and a potential target for antiviral strategies.
C3HC4 domain binding in NF-kB signaling and cell survival
Linear ubiquitination at damaged lysosomes induces local NF-kB activation and controls cell survival, a process dependent on RING domain-containing complexes. Dysregulation of this pathway can contribute to inflammatory disease and cancer cell survival.
C3HC4 domain binding in autophagy and neurodegeneration
LUBAC and OTULIN regulate autophagy initiation and maturation by mediating linear ubiquitination and stabilization of ATG13. Because autophagy dysfunction is linked to neurodegeneration, C3HC4 domain interactions may influence neuronal proteostasis.
C3HC4 domain binding in plant immunity
The IMMUNE-ASSOCIATED NUCLEOTIDE-BINDING 9 protein is a regulator of basal immunity in Arabidopsis thaliana, highlighting conserved roles of C3HC4-related proteins in defense signaling.
From C3HC4-type RING finger domain binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Is the C3HC4 domain required for E3 ligase activity? | Point mutation of zinc-coordinating cysteines/histidines |
| Does loss of the RING domain abolish antiviral function? | CRISPR knockout of the RING domain in TRIM21 |
| Can a tagged C3HC4 domain pull down binding partners? | Knock-in of an epitope tag at the endogenous locus |
| Does overexpression of a C3HC4 protein alter autophagy? | Overexpression cell lines and ATG13 stability assays |
| Which residues mediate binding to dysbindin? | Point mutation and co-immunoprecipitation |
| Does C3HC4 domain binding regulate NF-kB locally? | Knockout and knock-in models with NF-kB reporters |
How to Study the C3HC4-type RING finger domain binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Co-immunoprecipitation | Physical interaction between C3HC4 domain and partner | Validate RNF151-dysbindin binding |
| GST pull-down | Direct binding in vitro | Map domain requirements |
| CRISPR knockout screen | Genes required for C3HC4-dependent phenotype | Antiviral immunity |
| Site-directed mutagenesis | Role of zinc-coordinating residues | Domain folding and binding |
| Ubiquitin chain-specific antibodies | Linear vs. K48/K63 ubiquitination | LUBAC and OTULIN studies |
| Luciferase reporter | NF-kB transcriptional activity | Damaged lysosome signaling |
| Fluorescence microscopy | Subcellular localization of C3HC4 complexes | Lysosome and autophagy imaging |
| RNA-seq | Transcriptional changes upon C3HC4 perturbation | Immune gene expression in silkworm |
Co-immunoprecipitation and pull-down assays
Co-immunoprecipitation and GST pull-down assays are standard methods to detect C3HC4-type RING finger domain binding. These approaches can confirm interactions such as RNF151 with dysbindin and TRIM21 with viral or host proteins.
CRISPR-based genetic screens
Genome-wide CRISPR knockout screens can identify genes required for C3HC4 domain-dependent processes, such as antiviral restriction or NF-kB activation. Hits can be validated with point mutations in the RING domain.
Proteomics and ubiquitin chain analysis
Mass spectrometry-based proteomics can map ubiquitination sites and chain types downstream of C3HC4 domain binding. Linear ubiquitination assays are particularly relevant for LUBAC and OTULIN studies.
Imaging and reporter assays
Fluorescence microscopy and luciferase reporters can visualize localization and signaling outputs of C3HC4 domain interactions, such as local NF-kB activation at damaged lysosomes.
How CRISPR Can Be Used to Study GO:0055131 C3HC4-type RING finger domain binding
Knockout
CRISPR knockout of genes encoding C3HC4 domain-containing proteins or their binding partners can abolish domain-mediated interactions. For example, knocking out TRIM21 RING domain function eliminates anti-PRRSV activity, demonstrating the essential role of the C3HC4 domain in antiviral immunity. Knockout models are also useful for testing the requirement of LUBAC components in NF-kB activation.
Point Mutation
Point mutations that substitute zinc-coordinating cysteine or histidine residues in the C3HC4 consensus sequence disrupt domain folding and binding. Such mutations can be introduced by CRISPR base editing or homology-directed repair to test the specific contribution of the RING domain without deleting the entire protein.
Knock-in
Knock-in of epitope tags, fluorescent proteins, or affinity handles at the endogenous locus enables direct visualization and purification of C3HC4 domain complexes. This approach has been used to study RNF151 interactions with dysbindin and can be adapted to other C3HC4 proteins.
Overexpression
Overexpression of wild-type or mutant C3HC4 domain proteins can reveal gain-of-function phenotypes, such as altered autophagy or NF-kB signaling. Overexpression of LUBAC components or OTULIN has been used to dissect linear ubiquitination effects on ATG13 stability.
How EDITGENE Supports C3HC4-type RING finger domain binding Research
Researchers studying C3HC4-type RING finger domain binding-related genes often need to determine whether a candidate gene is causally involved in a specific pathway, whether a particular domain residue is required for binding, and how the interaction affects downstream signaling. EDITGENE provides end-to-end CRISPR services to answer these questions with publication-ready models.
Contact EDITGENE today to design your custom CRISPR model for C3HC4-type RING finger domain binding research.
Frequently Asked Questions About C3HC4-type RING finger domain binding
What is GO:0055131?
GO:0055131 is the Gene Ontology molecular function term for C3HC4-type RING finger domain binding, defined as binding to a C3HC4-type zinc finger domain of a protein.
What is a C3HC4-type RING finger domain?
It is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions and has the consensus sequence C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C.
What genes are involved in C3HC4-type RING finger domain binding?
Genes include TRIM21, RNF151, C-RZF, LUBAC components, OTULIN, and many C3HC4-type zinc finger genes identified in silkworm.
How is C3HC4-type RING finger domain binding related to ubiquitination?
Many proteins containing a C3HC4-type RING finger play a key role in the ubiquitination pathway, acting as E3 ligases that transfer ubiquitin to substrates.
What diseases are linked to C3HC4 domain interactions?
They are linked to antiviral immunity, NF-kB-driven inflammation, autophagy-related neurodegeneration, and plant basal immunity.
How can I study C3HC4 domain binding in the lab?
Common methods include co-immunoprecipitation, GST pull-down, CRISPR knockout, point mutation, and ubiquitin chain analysis.
What is the role of TRIM21 RING domain in antiviral immunity?
Porcine TRIM21 RING-finger E3 ubiquitin ligase is essential for anti-PRRSV activity, and its RING domain mediates critical interactions.
Does RNF151 bind dysbindin through its RING domain?
Yes, RNF151, a testis-specific RING finger protein, interacts with dysbindin, linking C3HC4 binding to testis biology.
How does LUBAC regulate autophagy?
LUBAC and OTULIN regulate autophagy initiation and maturation by mediating linear ubiquitination and stabilization of ATG13.
Can CRISPR be used to study C3HC4 domain function?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models enable causal dissection of C3HC4 domain interactions.
Conclusion
GO:0055131, C3HC4-type RING finger domain binding, is a central molecular function in ubiquitin signaling, antiviral immunity, autophagy, and NF-kB activation. The domain's zinc-coordinated fold provides a versatile platform for protein-protein recognition, and its dysfunction is linked to infection, inflammation, and cell survival defects. CRISPR-based models are powerful tools to dissect the causal roles of C3HC4 domain residues and their binding partners. EDITGENE offers comprehensive knockout, point-mutation, knock-in, overexpression, and screening services to accelerate this research.
References
- 1. Zein L et al.. 2025. Linear ubiquitination at damaged lysosomes induces local NFKB activation and controls cell survival.. Autophagy 21(5):1075-1095 PMID: 39744815
- 2. Chu Y et al.. 2021. LUBAC and OTULIN regulate autophagy initiation and maturation by mediating the linear ubiquitination and the stabilization of ATG13.. Autophagy 17(7):1684-1699 PMID: 32543267
- 3. Liu J et al.. 2026. Genome-wide identification and immunological expression analysis of the C3HC4-type zinc finger protein genes in the silkworm, Bombyx Mori.. BMC Genomics 27(1) PMID: 41772421
- 4. Wei Y et al.. 2021. Porcine TRIM21 RING-finger E3 ubiquitin ligase is essential for anti-PRRSV activity.. Vet Microbiol 256:109043 PMID: 33780804
- 5. Nian H et al.. 2007. RNF151, a testis-specific RING finger protein, interacts with dysbindin.. Arch Biochem Biophys 465(1):157-63 PMID: 17577571
- 6. Tranque P et al.. 1996. Identification and characterization of a RING zinc finger gene (C-RZF) expressed in chicken embryo cells.. Proc Natl Acad Sci U S A 93(7):3105-9 PMID: 8610176
- 7. Wang Y et al.. 2019. The IMMUNE-ASSOCIATED NUCLEOTIDE-BINDING 9 Protein Is a Regulator of Basal Immunity in Arabidopsis thaliana.. Mol Plant Microbe Interact 32(1):65-75 PMID: 29958083
