SMTL ID : 8ae0.1

Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-10-1-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain B: N.165, S.167, D.196, D.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.196 NAG-NAG.2: 4 residues within 4Å: Chain F: N.165, S.167, D.196, D.202 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.196 NAG-NAG.3: 3 residues within 4Å: Chain Q: N.48, S.50, D.51 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:S.50, Q:S.50

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 2 residues within 4Å: Chain G: N.370 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.370 NAG.5: 6 residues within 4Å: Chain G: L.368, N.370 Chain H: N.370, S.372 Ligands: NAG.4, NAG.6 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:N.370, H:S.372, H:S.372 Hydrophobic interactions: G:L.368 NAG.6: 6 residues within 4Å: Chain H: L.368, N.370 Chain I: N.370, S.372 Ligands: NAG.5, NAG.7 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.372, I:S.372 NAG.7: 5 residues within 4Å: Chain I: N.370 Chain J: N.370, S.372 Ligands: NAG.6, NAG.8 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:N.370, J:S.372, J:S.372 NAG.8: 5 residues within 4Å: Chain J: T.367, N.370 Chain K: N.370, S.372 Ligands: NAG.7 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:N.370, K:S.372, K:S.372 Hydrophobic interactions: J:T.367 NAG.9: 3 residues within 4Å: Chain L: K.365, N.370 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.370 NAG.10: 7 residues within 4Å: Chain L: N.370, S.372 Chain M: N.370, V.371, S.372 Ligands: NAG.9, NAG.11 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain L Hydrogen bonds: M:N.370, L:S.372 NAG.11: 6 residues within 4Å: Chain N: N.370, S.372 Chain O: L.368, N.370 Ligands: NAG.10, NAG.12 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:N.370 NAG.12: 4 residues within 4Å: Chain O: N.370, S.372 Ligands: NAG.11, NAG.13 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:S.372 NAG.13: 10 residues within 4Å: Chain N: Y.383 Chain P: L.368, N.370, S.372 Chain Q: R.4, R.20, I.22, E.34, N.36 Ligands: NAG.12 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain P Hydrogen bonds: Q:R.4, Q:R.4, Q:R.20, Q:N.36, P:N.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Q. et al., Cryomicroscopy reveals the structural basis for a flexible hinge motion in the immunoglobulin M pentamer. Nat Commun (2022)

Release Date

2022-10-26

Peptides

IgM Fab, light chain: AE
IgM Fab, heavy chain: BF
IgM C2-domain from mouse: CD
Immunoglobulin heavy constant mu: GHIJKLMNOP
Immunoglobulin J chain: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

E
S

B
H

F
Q

C
I

D
B

G
N

H
O

I
C

J
D

K
E

L
F

M
G

N
R

O
K

P
T

Q
J

IgM Fab, light chain

IgM Fab, heavy chain

IgM C2-domain from mouse

Immunoglobulin heavy constant mu

Immunoglobulin J chain

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