8URJ | pdb_00008urj

Cryo-EM structure of the HIV-1 nuclear export complex

• PDB DOI: https://doi.org/10.2210/pdb8URJ/pdb
• NAKB: 8URJ
• EM Map EMD-42494: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Homo sapiens, Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2023-10-26 Released: 2025-04-30 
• Deposition Author(s): Smith, A.M., Cheng, Y., Frankel, A.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director, Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Structure of the HIV-1 RNA Nuclear Export Complex Reveals Crm1 Versatility

Smith, A.M., Cheng, Y., Frankel, A.D., Li, Y., Velarde, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 422.31 kDa 
• Atom Count: 21,963 
• Modeled Residue Count: 2,642 
• Deposited Residue Count: 3,025 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1	A, C	1,062	Homo sapiens	Mutation(s): 0  Gene Names: XPO1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens) Explore O14980  Go to UniProtKB:  O14980
PHAROS:  O14980 GTEx:  ENSG00000082898

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rev HIV-1	B	92	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: Rev

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	D, F [auth H]	181	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Rev HIV-1	E	92	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P69718 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB3)) Explore P69718  Go to UniProtKB:  P69718

Entity ID: 5
Molecule	Chains	Length	Organism	Image
HIV-1 RRE	G	355	Human immunodeficiency virus 1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Smith, A.M., Cheng, Y., Frankel, A.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI170792
National Institutes of Health/Office of the Director	United States	OD020054
National Institutes of Health/Office of the Director	United States	OD021741
National Institutes of Health/Office of the Director	United States	OD026881
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release