Macromolecule Content

Total Structure Weight: 48.45 kDa
Atom Count: 3,376
Modelled Residue Count: 434
Deposited Residue Count: 454
Unique protein chains: 3

5OCY

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

PDB DOI: https://doi.org/10.2210/pdb5OCY/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-07-04 Released: 2018-07-04
Deposition Author(s): Dobritzsch, D., Ge, C., Holmdahl, R.
Funding Organization(s): Knut and Alice Wallenberg Foundation, Swedish Research Council

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 2.0 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

PubMed: 30152126 Search on PubMed
DOI: https://doi.org/10.1002/art.40698
Primary Citation of Related Structures:
5OCK, 5OCX, 5OCY, 5OD0, 5OD8, 5ODB

PubMed Abstract:

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPA E4 Fab fragment - heavy chain	A [auth H]	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPA E4 Fab fragment - light chain	B [auth L]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CII-C-48-CIT	C	18	Homo sapiens	Mutation(s): 0 Gene Names: COL2A1
UniProt & NIH Common Fund Data Resources
Find proteins for P02458 (Homo sapiens) Explore P02458 Go to UniProtKB: P02458
PHAROS: P02458
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02458
Protein Feature View Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	B [auth L]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN
CIR Query on CIR	C	L-PEPTIDE LINKING	C₆ H₁₃ N₃ O₃		ARG

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 = 46.13	α = 90
b = 99.048	β = 90
c = 100.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	KAW 2010.0148
Swedish Research Council	Sweden	2015-02662

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.