SMTL ID : 7fjn.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

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

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

2022-04-27

Peptides

Spike glycoprotein,Envelope glycoprotein: ABC
T6 heavy chain: DE
T6 light chain: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
I

F
J

G
L

Spike glycoprotein,Envelope glycoprotein

T6 heavy chain

T6 light chain

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