5OCY

Crystal structure of ACPA E4 in complex with CII-C-48-CIT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies.

Ge, C.Xu, B.Liang, B.Lonnblom, E.Lundstrom, S.L.Zubarev, R.A.Ayoglu, B.Nilsson, P.Skogh, T.Kastbom, A.Malmstrom, V.Klareskog, L.Toes, R.E.M.Rispens, T.Dobritzsch, D.Holmdahl, R.

(2019) Arthritis Rheumatol 71: 210-221

  • DOI: https://doi.org/10.1002/art.40698
  • Primary Citation of Related Structures:  
    5OCK, 5OCX, 5OCY, 5OD0, 5OD8, 5ODB

  • PubMed Abstract: 

    Anti-citrullinated protein antibodies (ACPAs) develop many years before the clinical onset of rheumatoid arthritis (RA). This study was undertaken to address the molecular basis of the specificity and cross-reactivity of ACPAs from patients with RA.


  • Organizational Affiliation

    Karolinska Institutet, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACPA E4 Fab fragment - heavy chainA [auth H]220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACPA E4 Fab fragment - light chainB [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CII-C-48-CIT18Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02458 (Homo sapiens)
Explore P02458 
Go to UniProtKB:  P02458
PHAROS:  P02458
GTEx:  ENSG00000139219 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02458
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
B [auth L]L-PEPTIDE LINKINGC5 H7 N O3GLN
CIR
Query on CIR
C
L-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.13α = 90
b = 99.048β = 90
c = 100.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSwedenKAW 2010.0148
Swedish Research CouncilSweden2015-02662

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 2.0: 2020-03-11
    Changes: Database references, Polymer sequence
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 3.1: 2024-01-17
    Changes: Refinement description