SMTL ID : 7t4s.1

CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: R.53, E.54, N.55 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: Y.61, N.62 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:N.62 NAG.3: 3 residues within 4Å: Chain A: A.648, N.700, T.702 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.700, A:T.702 NAG.4: 2 residues within 4Å: Chain A: H.190, N.192 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain D: A.199, N.200, N.201 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain D: S.72, N.118 Chain J: I.54 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain D Hydrophobic interactions: J:I.54 Hydrogen bonds: D:S.72, D:S.72 NAG.7: 4 residues within 4Å: Chain C: Y.130 Chain E: Y.52, N.81, E.84 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.130 NAG.8: 2 residues within 4Å: Chain F: N.157, Y.265 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain F: N.152 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.152

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain F: E.197, D.211, T.251, D.252, V.255 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.197, F:D.211, F:D.211, F:V.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kschonsak, M. et al., Structural basis for HCMV Pentamer receptor recognition and antibody neutralization. Sci Adv (2022)

Release Date

2022-03-23

Peptides

Envelope glycoprotein H: A
Envelope glycoprotein L: B
Envelope protein UL128: C
Envelope glycoprotein UL130: D
Envelope protein UL131A: E
Neuropilin-2: F
Fab 8I21 heavy chain: G
Fab 13H11 heavy chain: H
Fab 13H11 light chain: I
Fab 8I21 light chain: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
J

I
K

J
I

Envelope glycoprotein H

Envelope glycoprotein L

Envelope protein UL128

Envelope glycoprotein UL130

Envelope protein UL131A

Neuropilin-2

Fab 8I21 heavy chain

Fab 13H11 heavy chain

Fab 13H11 light chain

Fab 8I21 light chain

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