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 

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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: https://doi.org/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, 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
MoleculeChains Sequence LengthOrganismDetailsImage
IG GAMMA-1 CHAIN CA,
C [auth D]
207Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
PHAROS:  P01857
GTEx:  ENSG00000211896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01857
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01857-2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
52 KDA RO PROTEINB,
D [auth E]
181Homo sapiensMutation(s): 0 
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P19474 (Homo sapiens)
Explore P19474 
Go to UniProtKB:  P19474
PHAROS:  P19474
GTEx:  ENSG00000132109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19474
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseE [auth C],
F
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28663KH
GlyCosmos:  G28663KH
GlyGen:  G28663KH
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  (Full details and data files)

  • 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
  • Version 3.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary