Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 49.72 kDa 
• Atom Count: 3508 
• Residue Count: 403 
• Unique protein chains: 3

2FNJ

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

• DOI: 10.2210/pdb2FNJ/pdb

• Classification: PROTEIN TRANSPORT/SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 16498413 
• 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, 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CG2944-PF, isoform F	A	226	Drosophila melanogaster	Mutation(s): 0  Gene Names: gus, CG2944
Find proteins for A1Z6E0 (Drosophila melanogaster) Explore A1Z6E0  Go to UniProtKB:  A1Z6E0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 2	B	118	Mus musculus	Mutation(s): 0  Gene Names: Elob, Tceb2
Find proteins for P62869 (Mus musculus) Explore P62869  Go to UniProtKB:  P62869

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 1	C	96	Mus musculus	Mutation(s): 0  Gene Names: Eloc, Tceb1
Find proteins for P83940 (Mus musculus) Explore P83940  Go to UniProtKB:  P83940

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 = 50.308	α = 90
b = 82.489	β = 90
c = 118.966	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

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