2J6E

CRYSTAL STRUCTURE OF AN AUTOIMMUNE COMPLEX BETWEEN A HUMAN IGM RHEUMATOID FACTOR AND IGG1 FC REVEALS A NOVEL FC EPITOPE AND EVIDENCE FOR AFFINITY MATURATION

Structural Biology Knowledgebase: 2J6E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.223

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2J6E

Classification: IMMUNE SYSTEM

Total Structure Weight: 156037.77

Macromolecule Entities
Molecule Chains Length Organism Details
IG GAMMA-1 CHAIN C REGION A, B 232 Homo sapiens Fragment: FC DOMAIN, RESIDUES 99-330
Mutation: D270E
Gene Name(s): IGHG1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
IGM H, I 231 Homo sapiens
IGM L, M 234 Homo sapiens

Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDG
Query on NDG

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A, B BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUL
Query on FUL

A, B BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE (Synonym)
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CAC
Query on CAC

A CACODYLATE ION
dimethylarsinate (Synonym)
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A, B, M (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B, H ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.223
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 241.98 α = 90.00
b = 75.61 β = 91.13
c = 102.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-09-28
  • Released Date: 2007-04-10
  • Deposition author(s): Duquerroy, S., Stura, E.A., Bressanelli, S., Browne, H., Beale, D., Hamon, M., Casali, P., Vaney, M.-C., Rey, F.A., Sutton, B.J., Taussig, M.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4