Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 91.18 kDa 
• Atom Count: 6590 
• Modelled Residue Count: 776 
• Deposited Residue Count: 776 
• Unique protein chains: 2

2IWG

COMPLEX BETWEEN THE PRYSPRY DOMAIN OF TRIM21 AND IGG FC

• PDB DOI: 10.2210/pdb2IWG/pdb

• Classification: IMMUNOGLOBULIN DOMAIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-30 Released: 2007-03-27 
• Deposition Author(s): James, L.C., Keeble, A.H., Rhodes, D.A., Trowsdale, J.

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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 

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

• PubMed: 17400754 
• 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, 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.

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Organizational Affiliation: 

Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IG GAMMA-1 CHAIN C	A, C [auth D]	207	Homo sapiens	Mutation(s): 0  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
52 KDA RO PROTEIN	B, D [auth E]	181	Homo sapiens	Mutation(s): 0  Gene Names: TRIM21, RNF81, RO52, SSA1 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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D 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	E [auth C], F	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28663KH GlyCosmos:  G28663KH GlyGen:  G28663KH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	G [auth A], H [auth D]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N

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 = 112.49	α = 90
b = 112.49	β = 90
c = 194.609	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-30 
• Released Date: 2007-03-27 
Deposition Author(s): James, L.C., Keeble, A.H., Rhodes, D.A., Trowsdale, J.

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