SMTL ID : 7lbf.1

CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 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: 3 residues within 4Å: Chain C: N.348, A.351 Chain D: I.258 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: L.424, K.428, N.431, W.461 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN.3: 11 residues within 4Å: Chain C: N.160, E.164, Q.165, G.166, C.167, G.168, N.169, M.320, T.322, R.325 Ligands: NAG.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.166, C:R.325, C:N.169, C:G.168

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

NAG.4: 2 residues within 4Å: Chain A: H.190, N.192 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.67 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.55 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: A.648, L.698, N.700, T.702 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.62 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain B: N.74 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain C: N.85 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain C: N.101 Ligand excluded by PLIP NAG.12: 6 residues within 4Å: Chain C: N.155, R.159, I.371, Y.372 Chain D: N.240, I.269 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: F.170, R.216, N.217 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain C: N.240, T.242, K.243 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain C: N.365, T.367 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain C: N.383, T.385 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain C: N.452 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: I.104, N.128, T.130 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: N.169 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: Y.238 Chain D: S.56, Y.101, N.103 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain C: R.117 Chain D: I.147, S.171, Q.176, N.179 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kschonsak, M. et al., Structures of HCMV Trimer reveal the basis for receptor recognition and cell entry. Cell (2021)

Release Date

2021-03-10

Peptides

Envelope glycoprotein H: A
Envelope glycoprotein L: B
Envelope glycoprotein O: C
Isoform 3 of Platelet-derived growth factor receptor alpha: D
Fab 13H11 light chain: E
Fab 13H11 heavy chain: F
Fab MSL-109 light chain: G
Fab MSL-109 heavy chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Envelope glycoprotein H

Envelope glycoprotein L

Envelope glycoprotein O

Isoform 3 of Platelet-derived growth factor receptor alpha

Fab 13H11 light chain

Fab 13H11 heavy chain

Fab MSL-109 light chain

Fab MSL-109 heavy chain

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