SMTL ID : 2j6e.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- GAL- BMA- NAG- FUL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-BMA-NAG-FUL.1: 17 residues within 4Å: Chain A: F.26, F.28, P.29, P.30, K.31, E.43, T.45, V.47, V.49, D.50, Q.80, Y.81, N.82, R.86, K.119 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-BMA-NAG-FUL.2, NAG-NAG-BMA-MAN-NAG-GAL-BMA-NAG-FUL.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.81 Hydrogen bonds: A:Q.80, A:K.31, A:K.31, A:E.43, A:E.43, A:T.45, A:R.86, A:K.119, A:K.119 NAG-NAG-BMA-MAN-NAG-GAL-BMA-NAG-FUL.2: 15 residues within 4Å: Chain B: F.26, F.28, P.30, K.31, D.34, E.43, T.45, V.49, D.50, Q.80, N.82, R.86, K.119 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-BMA-NAG-FUL.1, NAG-NAG-BMA-MAN-NAG-GAL-BMA-NAG-FUL.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.25, B:Q.80, B:K.31, B:K.31, B:D.34, B:E.43, B:E.43, B:E.43, B:T.45, B:R.86, B:K.119

1 x CD: CADMIUM ION(Non-covalent)

CD.3: 3 residues within 4Å: Chain A: H.95, L.99, H.220 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.95, A:H.220

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: E.130, H.218 Ligands: CAC.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.130, A:E.130, A:H.218 ZN.11: 2 residues within 4Å: Chain B: H.53, E.79 No protein-ligand interaction detected (PLIP)

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 3 residues within 4Å: Chain A: E.130, H.218 Ligands: ZN.4 No protein-ligand interaction detected (PLIP)

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 8 residues within 4Å: Chain A: P.56, E.57, V.58, T.74, K.75, P.76, R.77, V.87 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.58, A:T.74, A:R.77, A:R.77 Hydrogen bonds: A:V.58, A:R.77 MPD.7: 5 residues within 4Å: Chain A: P.32, I.162, A.163, V.164 Ligands: MPD.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.32 Hydrogen bonds: A:V.164 MPD.8: 7 residues within 4Å: Chain A: I.162, T.178, T.179, P.180, P.181, L.191 Ligands: MPD.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.162, A:L.191 Hydrogen bonds: A:T.178 MPD.12: 1 residues within 4Å: Chain B: H.218 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.218 MPD.13: 3 residues within 4Å: Chain B: Y.176, K.177, T.178 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.176 Hydrogen bonds: B:K.177, B:K.177, B:T.178, B:T.178 MPD.16: 8 residues within 4Å: Chain D: G.55, K.56, G.57 Chain F: D.105, Y.107, G.122, G.123, K.125 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.105, F:G.123, F:K.125

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 6 residues within 4Å: Chain A: K.155, D.184, S.185, D.186 Chain B: N.175, T.196 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.175, A:S.185, A:D.186, A:D.186 Salt bridges: B:K.194 ACT.10: 6 residues within 4Å: Chain A: V.64, V.69, N.71, L.91, T.92, V.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.71, A:N.71 ACT.14: 6 residues within 4Å: Chain A: D.141 Chain B: Q.132, V.133, Y.134 Chain D: Y.46, N.69 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:V.133, D:Y.71 Salt bridges: B:K.224, A:K.145 ACT.15: 5 residues within 4Å: Chain C: P.53, K.56, G.57, L.58, E.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duquerroy, S. et al., Crystal structure of a human autoimmune complex between IgM rheumatoid factor RF61 and IgG1 Fc reveals a novel epitope and evidence for affinity maturation. J.Mol.Biol. (2007)

Release Date

2007-04-10

Peptides

IG GAMMA-1 CHAIN C REGION: AB
IGM: CD
IGM: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
I

E
L

F
M

IG GAMMA-1 CHAIN C REGION

IGM

IGM