2IWG

COMPLEX BETWEEN THE PRYSPRY DOMAIN OF TRIM21 AND IGG FC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report



Literature

Structural Basis for Pryspry-Mediated Tripartite Motif (Trim) Protein Function.

James, L.C.Keeble, A.H.Khan, Z.Rhodes, D.A.Trowsdale, J.

(2007) Proc Natl Acad Sci U S A 104: 6200

  • DOI: 10.1073/pnas.0609174104
  • Primary Citation of Related Structures:  
    2IWG

  • PubMed Abstract: 
  • The human tripartite motif (TRIM) family comprises 70 members, including HIV restriction factor TRIM5alpha and disease-associated proteins TRIM20 (pyrin) and TRIM21. TRIM proteins have conserved domain architecture but diverse cellular roles. Here, w ...

    The human tripartite motif (TRIM) family comprises 70 members, including HIV restriction factor TRIM5alpha and disease-associated proteins TRIM20 (pyrin) and TRIM21. TRIM proteins have conserved domain architecture but diverse cellular roles. Here, we describe how the C-terminal PRYSPRY domain mediates diverse TRIM functions. The crystal structure of TRIM21 PRYSPRY in complex with its target IgG Fc reveals a canonical binding interface comprised of two discrete pockets formed by antibody-like variable loops. Alanine scanning of this interface has identified the hot-spot residues that control TRIM21 binding to Fc; the same hot-spots control HIV/murine leukemia virus restriction by TRIM5alpha and mediate severe familial Mediterranean fever in TRIM20/pyrin. Characterization of the IgG binding site for TRIM21 PRYSPRY reveals TRIM21 as a superantigen analogous to bacterial protein A and suggests that an antibody bipolar bridging mechanism may contribute to the pathogenic accumulation of anti-TRIM21 autoantibody immune complex in autoimmune disease.


    Organizational Affiliation

    Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, UK. lcj@mrc-lmb.cam.ac.uk



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IG GAMMA-1 CHAIN CAD207Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
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Go to UniProtKB:  P01857
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PHAROS  P01857
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
52 KDA RO PROTEINBE181Homo sapiensMutation(s): 0 
Gene Names: TRIM21RNF81RO52SSA1
EC: 2.3.2.27
Find proteins for P19474 (Homo sapiens)
Explore P19474 
Go to UniProtKB:  P19474
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PHAROS  P19474
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, F
7 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download CCD File 
A, D
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.49α = 90
b = 112.49β = 90
c = 194.609γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-11-15
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary