3FEY | pdb_00003fey

Crystal structure of the CBC-importin alpha complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.238 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The molecular basis for the regulation of the cap-binding complex by the importins.

Dias, S.M.Wilson, K.F.Rojas, K.S.Ambrosio, A.L.Cerione, R.A.

(2009) Nat Struct Mol Biol 16: 930-937

  • DOI: https://doi.org/10.1038/nsmb.1649
  • Primary Citation Related Structures: 
    3FEX, 3FEY

  • PubMed Abstract: 

    The binding of capped RNAs to the cap-binding complex (CBC) in the nucleus, and their dissociation from the CBC in the cytosol, represent essential steps in RNA processing. Here we show how the nucleocytoplasmic transport proteins importin-alpha and importin-beta have key roles in regulating these events. As a first step toward understanding the molecular basis for this regulation, we determined a 2.2-A resolution X-ray structure for a CBC-importin-alpha complex that provides a detailed picture for how importin-alpha binds to the CBP80 subunit of the CBC. Through a combination of biochemical studies, X-ray crystallographic information and small-angle scattering experiments, we then determined how importin-beta binds to the CBC through its CBP20 subunit. Together, these studies enable us to propose a model describing how importin-beta stimulates the dissociation of capped RNA from the CBC in the cytosol following its nuclear export.


  • Organizational Affiliation
    • Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 160.77 kDa 
  • Atom Count: 10,746 
  • Modeled Residue Count: 1,286 
  • Deposited Residue Count: 1,413 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 1790Homo sapiensMutation(s): 0 
Gene Names: CBP80NCBPNCBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q09161 (Homo sapiens)
Explore Q09161 
Go to UniProtKB:  Q09161
PHAROS:  Q09161
GTEx:  ENSG00000136937 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09161
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 2156Homo sapiensMutation(s): 0 
Gene Names: CBP20NCBP2PIG55
UniProt & NIH Common Fund Data Resources
Find proteins for P52298 (Homo sapiens)
Explore P52298 
Go to UniProtKB:  P52298
PHAROS:  P52298
GTEx:  ENSG00000114503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52298
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit alpha-2467Homo sapiensMutation(s): 0 
Gene Names: KPNA2RCH1SRP1
UniProt & NIH Common Fund Data Resources
Find proteins for P52292 (Homo sapiens)
Explore P52292 
Go to UniProtKB:  P52292
PHAROS:  P52292
GTEx:  ENSG00000182481 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52292
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.238 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.842α = 90
b = 104.505β = 109.04
c = 108.558γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description