SMTL ID : 7fjo.1

Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex with three T6 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain G: N.262, E.263, N.264 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain G: N.598, T.600, Q.626 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain G: V.638, N.639, N.640 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain G: N.691, N.692, G.1113 Chain H: D.778 Ligand excluded by PLIP NAG.5: 6 residues within 4Å: Chain G: N.699, F.700, T.701, L.904, Q.908, Q.1053 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain G: N.783, S.785, Q.786 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain G: A.688, E.1054, K.1055, N.1056 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain G: I.1114, N.1116 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain H: N.313, Q.562 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain H: N.598, T.600, Q.626 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain H: H.637, V.638, N.639 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain H: N.691, N.692 Chain I: D.778 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain H: N.699, L.904, Q.908 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain H: N.783, S.785, Q.786 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain H: A.688, E.1054, K.1055, N.1056 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain H: I.1114, V.1115, N.1116 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain H: K.540 Chain I: N.264 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain I: R.310, N.313, I.314, T.315, Q.562, T.563 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain I: N.598, T.600 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain I: H.637, V.638, N.639 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain G: D.778 Chain I: N.691 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain I: N.699, T.701, L.904, Q.908 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain I: K.777, N.783, S.785, Q.786 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain I: A.688, E.1054, K.1055, N.1056 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain I: I.1114, N.1116 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, Q. et al., RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants. Iscience (2022)

Release Date

2022-04-13

Peptides

T6 heavy chain: ACD
T6 light chain: BEF
Spike glycoprotein: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

C
H

D
J

B
G

E
K

F
L

G
A

H
B

I
C

T6 heavy chain

T6 light chain

Spike glycoprotein

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