SMTL ID : 7nyc.1

cryoEM structure of 3C9-sMAC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.54 Å

Oligo State

hetero-1-1-1-3-1-1-1-mer

Ligands

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.1: 7 residues within 4Å: Chain A: A.337, L.338, K.339 Chain B: E.187, R.188, N.189, R.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.339, A:K.339

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.2: 4 residues within 4Å: Chain G: S.842, N.893, I.904, V.906 No protein-ligand interaction detected (PLIP)

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

MAN.3: 3 residues within 4Å: Chain A: P.13, W.14, Q.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.14, A:Q.24 MAN.4: 3 residues within 4Å: Chain B: S.15, W.16, R.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.16, B:R.31, B:R.31 MAN.5: 4 residues within 4Å: Chain B: W.497, K.508, R.510, E.532 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.443, B:R.510 MAN.7: 4 residues within 4Å: Chain C: N.13, W.14, R.29 Chain D: Q.471 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.13, C:W.14, C:R.29, C:R.29, D:Q.471 MAN.8: 3 residues within 4Å: Chain B: H.42 Chain C: W.512, P.545 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.512 MAN.9: 6 residues within 4Å: Chain C: I.128, L.461, M.462, N.465, W.515, R.528 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.465, C:R.528 MAN.12: 3 residues within 4Å: Chain D: P.26, W.27 Chain F: Q.471 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:W.27, D:W.27, F:Q.471

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain B: L.84, N.87, D.89, D.91, D.97, E.98 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.84, B:D.89, B:D.91, B:D.97, B:E.98 CA.11: 7 residues within 4Å: Chain C: L.83, C.85, N.86, D.88, D.90, D.96, E.97 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.88, C:D.90, C:D.96, C:D.96, C:E.97 CA.17: 6 residues within 4Å: Chain F: L.96, R.97, N.99, D.101, D.103, E.110 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:L.96, F:N.99, F:D.101, F:D.103, F:E.110

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

NAG.10: 3 residues within 4Å: Chain C: N.407, R.408, S.409 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.408 Hydrogen bonds: C:N.407, C:R.408, C:R.408 NAG.13: 6 residues within 4Å: Chain D: A.392, V.393, N.394 Chain F: E.201, A.202, F.203 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:A.392, D:V.393, F:E.201 NAG.15: 3 residues within 4Å: Chain E: E.221, Q.223, N.303 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.221, E:Q.223, E:N.303, E:N.303 NAG.16: 3 residues within 4Å: Chain F: A.392, V.393, N.394 No protein-ligand interaction detected (PLIP)

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.14: 4 residues within 4Å: Chain A: S.512 Chain E: T.17, C.18, C.57 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.512, 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 C7: A
Complement component C8 beta chain: B
Complement component C8 alpha chain: C
Complement component C9: DFI
Complement component C6: E
Complement C5: G
Complement component C8 gamma chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
G

F
H

I
I

E
B

G
A

H
F

Complement component C7

Complement component C8 beta chain

Complement component C8 alpha chain

Complement component C9

Complement component C6

Complement C5

Complement component C8 gamma chain

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