Macromolecule Content

Total Structure Weight: 94923.30
Atom Count: 6439
Residue Count: 804
Unique protein chains: 3

6ATF

HLA-DRB1*1402 in complex with Vimentin59-71

DOI: 10.2210/pdb6ATF/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens

Deposited: 2017-08-29 Released: 2017-09-13
Deposition Author(s): Scally, S.W., Ting, Y.T., Rossjohn, J.
Funding Organization(s): NHMRC, ARC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.9 Å
R-Value Free: 0.202
R-Value Work: 0.170

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis.

Scally, S.W., Law, S.C., Ting, Y.T., Heemst, J.V., Sokolove, J., Deutsch, A.J., Bridie Clemens, E., Moustakas, A.K., Papadopoulos, G.K., Woude, D.V., Smolik, I., Hitchon, C.A., Robinson, D.B., Ferucci, E.D., Bernstein, C.N., Meng, X., Anaparti, V., Huizinga, T., Kedzierska, K., Reid, H.H., Raychaudhuri, S., Toes, R.E., Rossjohn, J., El-Gabalawy, H., Thomas, R.

(2017) Ann. Rheum. Dis. 76: 1915-1923

PubMed: 28801345 Search on PubMed
DOI: 10.1136/annrheumdis-2017-211300
Primary Citation of Related Structures:
6ATZ, 6ATI

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	A, D	189	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens) Go to Gene View: HLA-DRA Go to UniProtKB: P01903
Protein Feature View Full Protein Feature View for P01903

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
MHC class II antigen	B, E	200	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Vimentin59-71	C, F	13	Homo sapiens	Mutation(s): 0 Gene Names: VIM
Find proteins for P08670 (Homo sapiens) Go to Gene View: VIM Go to UniProtKB: P08670
Protein Feature View Full Protein Feature View for P08670

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
EDO Query on EDO Download SDF File Download CCD File	B, E	1,2-ETHANEDIOL ETHYLENE GLYCOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
PGE Query on PGE Download SDF File Download CCD File	B	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
NAG Query on NAG Download SDF File Download CCD File	A, D	N-ACETYL-D-GLUCOSAMINE C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.9 Å
R-Value Free: 0.202
R-Value Work: 0.170
Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 66.980	α = 90.00
b = 77.770	β = 109.52
c = 94.540	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHENIX	phasing
PHENIX	refinement
SCALA	data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2017-08-29
Released Date: 2017-09-13
Deposition Author(s): Scally, S.W., Ting, Y.T., Rossjohn, J.

Funding Organization	Location	Grant Number
NHMRC, ARC	Australia	--

Revision History

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2017-10-18
Type: Database references

The RCSB PDB is funded by a grant (DBI-1338415) from the National Science Foundation, the National Institutes of Health, and the US Department of Energy.