2FNJ

Crystal structure of a B30.2/SPRY domain-containing protein GUSTAVUS in complex with Elongin B and Elongin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional insights into the B30.2/SPRY domain

Woo, J.S.Imm, J.H.Min, C.K.Kim, K.J.Cha, S.S.Oh, B.H.

(2006) EMBO J 25: 1353-1363

  • DOI: 10.1038/sj.emboj.7600994
  • Primary Citation of Related Structures:  
    2FNJ

  • PubMed Abstract: 
  • The B30.2/SPRY domain is present in approximately 700 eukaryotic (approximately 150 human) proteins, including medically important proteins such as TRIM5alpha and Pyrin. Nonetheless, the functional role of this modular domain remained unclear. Here, ...

    The B30.2/SPRY domain is present in approximately 700 eukaryotic (approximately 150 human) proteins, including medically important proteins such as TRIM5alpha and Pyrin. Nonetheless, the functional role of this modular domain remained unclear. Here, we report the crystal structure of an SPRY-SOCS box family protein GUSTAVUS in complex with Elongins B and C, revealing a highly distorted two-layered beta-sandwich core structure of its B30.2/SPRY domain. Ensuing studies identified one end of the beta-sandwich as the surface interacting with an RNA helicase VASA with a 40 nM dissociation constant. The sequence variation in TRIM5alpha responsible for HIV-1 restriction and most of the mutations in Pyrin causing familial Mediterranean fever map on this surface, implicating the corresponding region in many B30.2/SPRY domains as the ligand-binding site. The amino acids lining the binding surface are highly variable among the B30.2/SPRY domains, suggesting that these domains are protein-interacting modules, which recognize a specific individual partner protein rather than a consensus sequence motif.


    Organizational Affiliation

    Division of Molecular and Life Sciences, Department of Life Sciences, Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CG2944-PF, isoform FA226Drosophila melanogasterMutation(s): 0 
Gene Names: gusCG2944
Find proteins for A1Z6E0 (Drosophila melanogaster)
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Go to UniProtKB:  A1Z6E0
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor B polypeptide 2B118Mus musculusMutation(s): 0 
Gene Names: ElobTceb2
Find proteins for P62869 (Mus musculus)
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Go to UniProtKB:  P62869
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor B polypeptide 1C96Mus musculusMutation(s): 0 
Gene Names: ElocTceb1
Find proteins for P83940 (Mus musculus)
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Go to UniProtKB:  P83940
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.308α = 90
b = 82.489β = 90
c = 118.966γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-01-11 
  • Released Date: 2006-03-21 
  • Deposition Author(s): Woo, J.S., Oh, B.H.

Revision History 

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description