SMTL ID : 7nyd.1

cryoEM structure of 2C9-sMAC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.27 Å

Oligo State

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

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: E.187, N.189, R.227 Chain D: F.307, A.337 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain B: N.407, R.408 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 4 residues within 4Å: Chain H: S.842, N.891, N.893, I.904 No protein-ligand interaction detected (PLIP)

6 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.4: 4 residues within 4Å: Chain A: E.440, K.444, N.499, W.500 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.444, A:N.499, A:W.500, A:W.500 MAN.5: 2 residues within 4Å: Chain A: W.19, R.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.19, A:R.29, A:R.29 MAN.7: 2 residues within 4Å: Chain B: N.13, W.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.13, B:W.14, B:W.14 MAN.8: 3 residues within 4Å: Chain A: H.42 Chain B: W.512, R.530 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.530, B:R.530, A:H.42 MAN.11: 2 residues within 4Å: Chain C: W.27 Chain F: Q.471 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.471 MAN.13: 6 residues within 4Å: Chain D: E.424, L.427, D.428, D.431, W.484, R.497 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.424, D:D.431, D:W.484, D:W.484, D:R.497

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: L.84, N.87, D.89, D.91, D.97, E.98 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.84, A:D.89, A:D.91, A:D.97, A:E.98 CA.9: 6 residues within 4Å: Chain B: L.83, N.86, D.88, D.90, D.96, E.97 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.83, B:D.88, B:D.90, B:D.96, B:E.97 CA.12: 6 residues within 4Å: Chain C: R.97, C.98, N.99, G.100, D.101, D.103 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.103 CA.17: 9 residues within 4Å: Chain F: L.96, R.97, N.99, G.100, D.101, N.102, D.103, D.109, E.110 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:L.96, F:R.97, F:D.103, F:D.109, F:E.110

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

NAG.10: 5 residues within 4Å: Chain C: K.349, N.394, T.396 Chain F: Q.199, E.201 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.349, C:T.396, C:T.396, C:T.396 NAG.14: 4 residues within 4Å: Chain E: N.217, E.221, N.303, T.305 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.217, E:E.221, E:T.305, E:T.305 NAG.16: 3 residues within 4Å: Chain F: N.394, T.396, S.397 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.394

1 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.15: 4 residues within 4Å: Chain D: S.512 Chain E: T.17, C.18, C.57 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Menny, A. et al., Structural basis of soluble membrane attack complex packaging for clearance. Nat Commun (2021)

Release Date

2021-10-06

Peptides

Complement component C8 beta chain: A
Complement component C8 alpha chain: B
Complement component C9: CF
Complement component C7: D
Complement component C6: E
Complement component C8 gamma chain: G
Complement C5: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
G

F
H

D
C

E
B

G
F

H
A

Complement component C8 beta chain

Complement component C8 alpha chain

Complement component C9

Complement component C7

Complement component C6

Complement component C8 gamma chain

Complement C5

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