SMTL ID : 7tb8.1

Cryo-EM structure of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 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 A: N.318, P.566, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.704, L.909, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.704, L.909, Q.1058 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.909 NAG-NAG.8: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.704, L.909, Q.1058 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.909

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: N.267, E.268, N.269 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.696, G.1118 Chain B: D.783 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.1061, F.1062 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.590, T.591 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: E.268, N.269 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1061 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.318 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: E.268, N.269 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: F.46, N.48, P.618 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: C.2, N.4, N.124 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: T.95, N.221 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.151, N.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Science (2022)

Release Date

2022-03-30

Peptides

Spike glycoprotein: ABC
The heavy chain of SARS-CoV-2 antibody A19-61.1: DFJ
The light chain of SARS-COV-2 antibody A19-61.1: EGK
The heavy chain of SARS-CoV-2 antiboddy antibody B1-182.1: H
The light chain of SARS-COV-2 antibody B1-182.1: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

J
J

E
E

G
G

K
K

H
H

I
L

Spike glycoprotein

The heavy chain of SARS-CoV-2 antibody A19-61.1

The light chain of SARS-COV-2 antibody A19-61.1

The heavy chain of SARS-CoV-2 antiboddy antibody B1-182.1

The light chain of SARS-COV-2 antibody B1-182.1

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