GO:1901707 leptomycin B binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1901707 (leptomycin B binding) is a molecular function defined as binding to leptomycin B, a Streptomyces metabolite that covalently modifies CRM1 (Exportin 1).
• The principal characterized leptomycin B binding protein is CRM1/XPO1, whose cysteine 528 is the covalent target of the drug.
• Leptomycin B binding inhibits CRM1-dependent nuclear export of proteins bearing leucine-rich nuclear export signals, causing their nuclear accumulation.
• Leptomycin B binding also alters CRM1 subcellular distribution, providing a readout for target engagement.
• The term is experimentally probed by nuclear export assays, imaging of shuttling proteins, and ribosome export reporters [2,4,5,6,7].
• Because CRM1 is the sole essential exportin for many cargos, leptomycin B binding is a widely used tool to dissect nucleocytoplasmic trafficking in cancer and viral biology [1,3,6].
Description
GO:1901707, leptomycin B binding, is a molecular function term describing the selective non-covalent and covalent interaction of a protein with leptomycin B, a unsaturated, branched-chain fatty acid produced by Streptomyces. The best-characterized leptomycin B binding protein is CRM1 (also called Exportin 1 or XPO1), a karyopherin that mediates nuclear export of proteins carrying leucine-rich nuclear export signals (NES). Kudo et al. showed that leptomycin B directly binds CRM1 and inhibits signal-mediated nuclear export, establishing the drug as a specific chemical probe for CRM1 function. Because CRM1 is the major exportin for many tumor suppressors and cell-cycle regulators, leptomycin B binding has become a standard tool in cell biology to test whether a protein shuttles between nucleus and cytoplasm [3,4,5,6,7]. Researchers use leptomycin B binding assays to validate nuclear export signals, to map CRM1-cargo interfaces, and to study viral and cellular nucleocytoplasmic transport [2,6]. The term is therefore central to studies of nuclear export, drug-target engagement, and the pharmacology of CRM1 inhibitors.
leptomycin B binding At A Glance
| GO ID | GO:1901707 |
|---|---|
| GO term | leptomycin B binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to leptomycin B, a CRM1 inhibitor that blocks NES-dependent nuclear export |
| Primary binding protein | CRM1/XPO1, via covalent modification of cysteine 528 |
| Cellular consequence | Nuclear accumulation of NES-containing cargo proteins and altered CRM1 distribution [1,3] |
| Experimental readout | Nuclear export assays, imaging of shuttling reporters, ribosome export reporters [2,4,5,6,7] |
| Disease relevance | CRM1 is implicated in cancer and viral nuclear export pathways [1,3,6] |
What Is GO:1901707?
Leptomycin B binding (GO:1901707) is the molecular function of selectively interacting with leptomycin B, a microbial metabolite that forms a covalent adduct with the CRM1 cysteine 528 residue and blocks CRM1-dependent nuclear export. In practice, the term covers both the physical binding event and the functional consequence of target engagement, namely inhibition of NES-dependent nuclear export and altered CRM1 localization [1,3].
Why Is leptomycin B binding Important in Cell Biology?
Leptomycin B binding is important because it provides a specific chemical handle to interrogate CRM1-dependent nuclear export, a process that controls the localization of tumor suppressors, cell-cycle regulators, and viral ribonucleoproteins [1,3,6]. The term is also a benchmark for target engagement in drug discovery, since leptomycin B binding is the defining interaction of CRM1 inhibitors. In addition, leptomycin B binding is used to validate nuclear export signals and to study nucleocytoplasmic shuttling of proteins such as STAT2, N4BP1, UPF1, and viral matrix proteins [4,5,6,7].
• Defines the molecular interaction of leptomycin B with CRM1, the major nuclear export receptor.
• Provides a pharmacological tool to block NES-dependent nuclear export in living cells.
• Enables validation of leucine-rich nuclear export signals in candidate proteins [4,5,7].
• Links to cancer biology because CRM1 exports tumor suppressors and cell-cycle regulators [1,3].
• Used to study viral nuclear export, including orthomyxovirus vRNP export.
• Supports drug discovery by confirming target engagement of CRM1 inhibitors.
• Helps dissect nucleocytoplasmic shuttling of RNA-binding proteins such as UPF1.
• Provides a readout for CRM1 subcellular redistribution after drug treatment.
• Facilitates ribosome export studies using reporter systems.
• Connects to stress and ubiquitin-like protein biology through N4BP1 shuttling.
Molecular Mechanism of leptomycin B binding
Covalent target engagement of CRM1
In simple terms: Leptomycin B sticks to CRM1 and blocks its export function.
Kudo et al. demonstrated that leptomycin B directly binds CRM1 and inhibits signal-mediated nuclear export. The interaction is covalent and involves cysteine 528 of CRM1, which is the critical residue for leptomycin B sensitivity. This binding event is the defining molecular function of GO:1901707 and explains why leptomycin B is a specific CRM1 inhibitor.
Inhibition of NES-dependent nuclear export
In simple terms: When leptomycin B binds CRM1, proteins that should leave the nucleus stay inside.
CRM1 mediates nuclear export of proteins carrying leucine-rich nuclear export signals. Leptomycin B binding prevents this export, causing nuclear accumulation of NES-containing cargoes. This functional consequence is widely used to test whether a protein is a CRM1 cargo [4,5,7].
Altered CRM1 subcellular distribution
In simple terms: Leptomycin B changes where CRM1 itself is located in the cell.
Rahmani et al. showed that leptomycin B alters the subcellular distribution of CRM1, providing a visual readout of leptomycin B binding and target engagement. This redistribution is a useful marker in imaging-based assays of CRM1 inhibition.
Cargo-specific effects on shuttling proteins
In simple terms: Different cargo proteins respond differently when leptomycin B binds CRM1.
Leptomycin B binding blocks nuclear export of STAT2, N4BP1, UPF1, and viral matrix proteins, as shown by nuclear accumulation assays [4,5,6,7]. These cargo-specific effects demonstrate that leptomycin B binding is a versatile tool for studying nucleocytoplasmic trafficking [4,5,6,7].
Ribosome export as a functional readout
In simple terms: Leptomycin B binding can be monitored by watching ribosomes leave the nucleus.
Lo et al. reengineered ribosome export and used leptomycin B sensitivity to probe CRM1-dependent export pathways. This provides a genetic and cell-biological system to study leptomycin B binding in the context of ribosome biogenesis and export.
Key Genes Involved in GO:1901707 leptomycin B binding
The following genes and proteins are experimentally linked to leptomycin B binding and CRM1-dependent nuclear export.
| Gene | Major Role | Research Relevance |
|---|---|---|
| XPO1 (CRM1) | Primary leptomycin B binding protein; nuclear export receptor | Target engagement, nuclear export assays, cancer biology [1,3] |
| STAT2 | NES-containing cargo that accumulates in nucleus upon leptomycin B binding | Interferon signaling and nuclear trafficking studies |
| N4BP1 | Nucleocytoplasmic shuttling protein sensitive to leptomycin B | Stress and ubiquitin-like protein aggregate recognition |
| UPF1 | RNA-binding protein that shuttles independently of RNA binding and ATPase activity | Nonsense-mediated decay and nuclear export studies |
| Matrix protein (orthomyxovirus) | Viral protein involved in vRNP nuclear export | Viral nuclear export and leptomycin B sensitivity |
| UNC5b | Netrin-1 receptor linked to post-stroke ferroptosis | Context for CRM1-related trafficking in neuronal injury |
| Ribosome export reporters | Engineered systems to monitor CRM1-dependent export | Functional readout of leptomycin B binding |
| CRM1 cysteine 528 | Critical residue for leptomycin B covalent binding | Mutational analysis of drug sensitivity |
| NES-containing cargoes | Proteins with leucine-rich nuclear export signals | Validation of export signals using leptomycin B |
| BACH1 | Transcription factor linked to ferroptosis and oxidative stress | Downstream context of Netrin-1/UNC5b signaling |
| AMPK | Kinase pathway in Netrin-1/UNC5b signaling | Metabolic stress and neuronal survival |
| CRM1 inhibitor targets | Proteins whose export is blocked by leptomycin B | Drug discovery and target engagement |
| Nuclear export machinery | Karyopherins and RanGTP system | Mechanistic studies of nucleocytoplasmic transport |
| Viral vRNP complexes | Ribonucleoprotein complexes exported via CRM1 | Antiviral target studies |
| Shuttling RNA-binding proteins | Proteins that move between nucleus and cytoplasm | RNA processing and localization studies |
How Is leptomycin B binding Regulated?
Leptomycin B binding is regulated at the level of CRM1 availability and cysteine 528 integrity, since mutation of this residue abolishes drug sensitivity. CRM1 subcellular distribution is also dynamically regulated, and leptomycin B treatment alters this distribution. In addition, cargo-specific factors such as RNA-binding activity or ATPase activity can influence shuttling independently of leptomycin B binding, as shown for UPF1.
leptomycin B binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| XPO1 (CRM1) | Cancer, nuclear export dysregulation | CRM1 knockout or C528S point mutation cells |
| STAT2 | Interferon signaling and viral infection | STAT2 knockout with leptomycin B treatment |
| N4BP1 | Heat shock and NEDD8 aggregate recognition | N4BP1 knockout or tagged knock-in |
| UPF1 | Nonsense-mediated decay and RNA processing | UPF1 knockout with leptomycin B |
| Viral matrix protein | Orthomyxovirus vRNP export | Viral infection with leptomycin B |
Cancer and CRM1 inhibition
CRM1 is the primary leptomycin B binding protein and exports tumor suppressors and cell-cycle regulators. Leptomycin B binding therefore blocks a key nuclear export pathway that is dysregulated in cancer [1,3]. CRM1 inhibitors are being explored as anticancer agents, and leptomycin B binding serves as a benchmark for target engagement.
Viral nuclear export
Leptomycin B binding inhibits CRM1-dependent export of viral ribonucleoproteins, as shown for a tick-borne orthomyxovirus matrix protein. This links leptomycin B binding to antiviral strategies that target nuclear export.
Neurodegeneration and stress responses
N4BP1 is a nucleocytoplasmic shuttling protein that recognizes NEDD8 aggregates under heat shock, and its localization is sensitive to leptomycin B. Netrin-1/UNC5b signaling, which involves AMPK and BACH1, is linked to post-stroke neuronal ferroptosis. These findings connect leptomycin B binding to stress and neuronal injury pathways [5,8].
From leptomycin B binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does a gene product bind leptomycin B? | CRM1 knockout cells reconstituted with wild-type or C528S mutant |
| Is a protein a CRM1 cargo? | Leptomycin B treatment followed by imaging of nuclear accumulation [4,5,7] |
| Does a mutation alter leptomycin B sensitivity? | Point mutation at CRM1 cysteine 528 |
| Can we track CRM1 distribution? | Tagged knock-in of CRM1 with fluorescent protein |
| Does overexpression change export? | Overexpression of NES-containing cargo |
| Can we screen for export defects? | CRISPR library screening with leptomycin B selection |
How to Study the leptomycin B binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Fluorescence microscopy | Nuclear vs cytoplasmic localization of cargo [4,5,7] | Validation of CRM1 cargoes [4,5,7] |
| Ribosome export reporter | CRM1-dependent ribosome export | Functional readout of leptomycin B binding |
| Biochemical binding assay | Direct leptomycin B-CRM1 interaction | Target engagement studies |
| Subcellular fractionation | Protein distribution changes [3,5] | Cargo identification [3,5] |
| Mutational analysis | Role of CRM1 cysteine 528 | Drug sensitivity testing |
| High-content imaging | CRM1 redistribution | Screening for export inhibitors |
| CRISPR screening | Genes required for export | Pathway discovery |
Imaging of nucleocytoplasmic shuttling
Fluorescence microscopy of GFP-tagged cargo proteins before and after leptomycin B treatment is a standard method to assess leptomycin B binding and CRM1-dependent export [4,5,7]. Nuclear accumulation indicates inhibition of export [4,5,7].
Nuclear export reporter assays
Engineered ribosome export reporters and NES-reporter constructs allow quantitative measurement of CRM1-dependent export and leptomycin B sensitivity. These assays can be adapted to high-throughput screening.
Biochemical binding assays
Direct binding of leptomycin B to CRM1 can be assessed by biochemical methods, as originally shown by Kudo et al.. Mutational analysis of cysteine 528 confirms specificity.
Proteomics and subcellular fractionation
Subcellular fractionation followed by mass spectrometry can identify proteins whose localization changes upon leptomycin B binding [3,5]. This approach helps define cargo repertoires [3,5].
How CRISPR Can Be Used to Study GO:1901707 leptomycin B binding
Knockout
CRISPR knockout of XPO1 (CRM1) abolishes leptomycin B binding and nuclear export, providing a negative control for export assays. Knockout of cargo genes such as STAT2, N4BP1, or UPF1 helps determine whether their shuttling depends on CRM1 [4,5,7].
Point Mutation
A C528S point mutation in CRM1 abolishes leptomycin B binding and drug sensitivity, making it a key tool to confirm target specificity. Point mutations in cargo NES sequences can also be introduced to test export signal function.
Knock-in
Tagged knock-in of CRM1 or cargo proteins with fluorescent or affinity tags enables live-cell imaging of leptomycin B binding effects and CRM1 redistribution. Knock-in of reporter cassettes can create sensitive export readouts.
Overexpression
Overexpression of NES-containing cargoes or CRM1 can be used to test whether leptomycin B binding is saturable and to amplify export signals. Overexpression of viral matrix proteins can model viral nuclear export.
How EDITGENE Supports leptomycin B binding Research
Researchers studying leptomycin B binding-related genes often need to determine whether a candidate gene is causally involved in CRM1-dependent nuclear export or is merely a bystander. EDITGENE provides CRISPR-engineered cell models to test these hypotheses with precision.
Contact EDITGENE today to design your custom CRISPR model for leptomycin B binding research.
Frequently Asked Questions About leptomycin B binding
What is leptomycin B binding?
Leptomycin B binding (GO:1901707) is the molecular function of binding to leptomycin B, a Streptomyces metabolite that covalently modifies CRM1 and blocks nuclear export.
What genes are involved in leptomycin B binding?
The primary gene is XPO1 (CRM1), which encodes the leptomycin B target; cargo genes include STAT2, N4BP1, and UPF1 [1,4,5,7].
How does leptomycin B inhibit nuclear export?
Leptomycin B binds CRM1 at cysteine 528 and prevents NES-dependent nuclear export, causing cargo accumulation in the nucleus.
What is the role of CRM1 in leptomycin B binding?
CRM1 is the direct binding protein for leptomycin B and the major nuclear export receptor.
Which diseases are linked to leptomycin B binding?
CRM1-dependent export is linked to cancer and viral infections, and leptomycin B binding is used to study these pathways [1,3,6].
How can I study leptomycin B binding in the lab?
Common methods include fluorescence imaging of cargo shuttling, ribosome export reporters, and biochemical binding assays [1,2,4,5,7].
What is the GO ID for leptomycin B binding?
The GO ID is GO:1901707.
Can CRISPR be used to study leptomycin B binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models can test CRM1 function and drug sensitivity [1,3].
What are the synonyms for leptomycin B binding?
There are no synonyms listed for GO:1901707.
Why is leptomycin B binding important for cancer research?
CRM1 exports tumor suppressors, and leptomycin B binding blocks this export, making it a tool for studying CRM1 inhibitors in cancer [1,3].
Conclusion
GO:1901707 leptomycin B binding defines a specific molecular interaction with CRM1 that has become a cornerstone of nuclear export research. From validating nuclear export signals to studying viral ribonucleoprotein export and cancer-related trafficking, leptomycin B binding provides a precise pharmacological tool [1,3,6]. CRISPR-engineered cell models from EDITGENE can help researchers dissect the genes and mechanisms underlying this function.
References
- 1. Kudo N et al.. 1998. Leptomycin B inhibition of signal-mediated nuclear export by direct binding to CRM1.. Exp Cell Res 242(2):540-7 PMID: 9683540
- 2. Lo KY et al.. 2009. Reengineering ribosome export.. Mol Biol Cell 20(5):1545-54 PMID: 19144820
- 3. Rahmani K et al.. 2017. Leptomycin B alters the subcellular distribution of CRM1 (Exportin 1).. Biochem Biophys Res Commun 488(2):253-258 PMID: 28412356
- 4. Banninger G et al.. 2004. STAT2 nuclear trafficking.. J Biol Chem 279(38):39199-206 PMID: 15175343
- 5. Guo X et al.. 2025. N4BP1 is a nucleocytoplasmic shuttling protein and recognizes aggregates of the ubiquitin-like protein NEDD8 to protect cells under heat shock.. J Biol Chem 301(9):110511 PMID: 40701250
- 6. Swenson VA et al.. 2025. Involvement of a tick-borne orthomyxovirus matrix protein in vRNP nuclear export.. J Virol 99(12):e0149425 PMID: 41329001
- 7. Nasif S et al.. 2025. UPF1 shuttles between nucleus and cytoplasm independently of its RNA-binding and ATPase activities.. RNA 31(12):1872-1885 PMID: 41057268
- 8. Luo Y et al.. 2025. Netrin-1 binding to UNC5b improves post-stroke neuronal ferroptosis via AMPK-BACH1 pathway.. Eur J Pharmacol 998:177507 PMID: 40086580
