3LWW | pdb_00003lww

Structure of an open and closed conformation of Human Importin Beta bound to the Snurportin1 IBB-domain trapped in the same crystallographic asymmetric unit

• PDB DOI: https://doi.org/10.2210/pdb3LWW/pdb

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


• Deposited: 2010-02-24 Released: 2010-06-02 
• Deposition Author(s): Bhardwaj, A., Cingolani, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.313 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.266 (Depositor) 

Starting Model: experimental

Literature

Conformational selection in the recognition of the snurportin importin beta binding domain by importin beta.

Bhardwaj, A., Cingolani, G.

(2010) Biochemistry 49: 5042-5047

• PubMed: 20476751 
• DOI: https://doi.org/10.1021/bi100292y
• Primary Citation Related Structures: 
  3LWW


• PubMed Abstract: 
  

  The structural flexibility of beta-karyopherins is critical to mediate the interaction with transport substrates, nucleoporins, and the GTPase Ran. In this paper, we provide structural evidence that the molecular recognition of the transport adaptor snurportin by importin beta follows the population selection mechanism. We have captured two drastically different conformations of importin beta bound to the snurportin importin beta binding domain trapped in the same crystallographic asymmetric unit. We propose the population selection may be a general mechanism used by beta-karyopherins to recognize transport substrates.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 204.57 kDa 
• Atom Count: 14,127 
• Modeled Residue Count: 1,809 
• Deposited Residue Count: 1,832 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin subunit beta-1	A, C	876	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
Snurportin-1	B, D	40	Homo sapiens	Mutation(s): 0  Gene Names: SNUPN
UniProt & NIH Common Fund Data Resources
Find proteins for O95149 (Homo sapiens) Explore O95149  Go to UniProtKB:  O95149
GTEx:  ENSG00000169371

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.313 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.266 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.65	α = 90
b = 101.735	β = 110.88
c = 101.963	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Bhardwaj, A., Cingolani, G.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description