9YB5 | pdb_00009yb5

Cryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex

• PDB DOI: https://doi.org/10.2210/pdb9YB5/pdb
• EM Map EMD-72749: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-16 Released: 2025-12-10 
• Deposition Author(s): Ko, Y., Cingolani, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex

Ko, Y., Cingolani, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.36 kDa 
• Atom Count: 6,402 
• Modeled Residue Count: 804 
• Deposited Residue Count: 804 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin subunit beta-1	A [auth B]	458	Homo sapiens	Mutation(s): 0  Gene Names: KPNB1, NTF97
UniProt & NIH Common Fund Data Resources
Find proteins for Q14974 (Homo sapiens) Explore Q14974  Go to UniProtKB:  Q14974
PHAROS:  Q14974 GTEx:  ENSG00000108424

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	B [auth D]	210	Homo sapiens	Mutation(s): 0  Gene Names: RAN, ARA24, OK/SW-cl.81 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens) Explore P62826  Go to UniProtKB:  P62826
PHAROS:  P62826 GTEx:  ENSG00000132341

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran-specific GTPase-activating protein	C	136	Homo sapiens	Mutation(s): 0  Gene Names: RANBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P43487 (Homo sapiens) Explore P43487  Go to UniProtKB:  P43487
PHAROS:  P43487 GTEx:  ENSG00000099901

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	E [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Ko, Y., Cingolani, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release