SMTL ID : 8ae2.1

Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 5

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-10-2-1-2-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 G: N.165, S.167, D.196, D.202 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.196 NAG-NAG.2: 3 residues within 4Å: Chain I: N.48, S.50, D.51 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.50, I:S.50 NAG-NAG.3: 4 residues within 4Å: Chain N: N.165, S.167, D.196, D.202 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:D.196

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

NAG.4: 6 residues within 4Å: Chain B: N.370, S.372 Chain M: L.368, N.370 Ligands: NAG.5, NAG.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.372, B:S.372 NAG.5: 4 residues within 4Å: Chain C: N.370, S.372 Ligands: NAG.4, NAG.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.370, C:S.372, C:S.372 NAG.6: 5 residues within 4Å: Chain C: T.367, N.370 Chain D: N.370, S.372 Ligands: NAG.5 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.370, D:S.372, D:S.372 Hydrophobic interactions: C:T.367 NAG.7: 3 residues within 4Å: Chain E: K.365, N.370 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.365, E:N.370 NAG.8: 7 residues within 4Å: Chain E: N.370, S.372 Chain F: N.370, V.371, S.372 Ligands: NAG.7, NAG.12 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.372, F:N.370 NAG.9: 4 residues within 4Å: Chain J: N.370, S.372 Ligands: NAG.12, NAG.13 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.372 NAG.10: 2 residues within 4Å: Chain L: N.370 Ligands: NAG.11 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.370 NAG.11: 6 residues within 4Å: Chain L: L.368, N.370 Chain M: N.370, S.372 Ligands: NAG.4, NAG.10 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain L Hydrogen bonds: M:N.370, M:S.372, M:S.372 Hydrophobic interactions: L:L.368 NAG.12: 6 residues within 4Å: Chain J: L.368, N.370 Chain O: N.370, S.372 Ligands: NAG.8, NAG.9 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.370 NAG.13: 10 residues within 4Å: Chain I: R.4, R.20, I.22, E.34, N.36 Chain O: Y.383 Chain Q: L.368, N.370, S.372 Ligands: NAG.9 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain Q Hydrogen bonds: I:R.4, I:R.4, I:R.20, I:N.36, Q: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 C2-domain from mouse: AH
Immunoglobulin heavy constant mu: BCDEFJLMOQ
IgM Fab, heavy chain: GN
Immunoglobulin J chain: I
IgM Fab, light chain: KP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

H
I

B
C

C
D

D
E

E
F

F
G

J
K

L
N

M
O

O
R

Q
T

G
H

N
Q

I
J

K
L

P
S

IgM C2-domain from mouse

Immunoglobulin heavy constant mu

IgM Fab, heavy chain

Immunoglobulin J chain

IgM Fab, light chain

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