SMTL ID : 7xq8.1

Structure of human B-cell antigen receptor of the IgM isotype

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

14 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 2 residues within 4Å: Chain A: T.411, N.412 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: Q.347, N.349 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.347, A:Q.347, A:N.349 NAG.3: 5 residues within 4Å: Chain A: R.363, F.365, L.385, T.387, N.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.419 NAG.4: 2 residues within 4Å: Chain C: T.411, N.412 No protein-ligand interaction detected (PLIP) NAG.5: 4 residues within 4Å: Chain C: R.363, T.387, H.417, N.419 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.387 Hydrogen bonds: C:R.363, C:R.363 NAG.6: 5 residues within 4Å: Chain C: E.291, M.334, T.336, Q.347, N.349 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.291, C:E.291, C:T.336, C:T.336, C:N.349 NAG.7: 2 residues within 4Å: Chain E: N.63, T.65 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain E: N.97, S.99, H.100 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.97, E:S.99, E:S.99 NAG.9: 1 residues within 4Å: Chain E: N.57 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.57 NAG.10: 3 residues within 4Å: Chain E: Q.53, P.87, N.88 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.88 NAG.11: 1 residues within 4Å: Chain E: N.112 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain C: Q.510 Chain E: N.73 Chain F: W.47 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:N.73, C:Q.510 NAG.13: 2 residues within 4Å: Chain F: N.101, E.102 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain F: N.73 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, Q. et al., Cryo-EM structure of the human IgM B cell receptor. Science (2022)

Release Date

2022-08-17

Peptides

Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu: AC
Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant: BD
B-cell antigen receptor complex-associated protein alpha chain: E
B-cell antigen receptor complex-associated protein beta chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
v

B
L

D
R

E
A

F
B

Membrane

We predict this structure to be a membrane protein.
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Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu

Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant

B-cell antigen receptor complex-associated protein alpha chain

B-cell antigen receptor complex-associated protein beta chain