SMTL ID : 6wxl.1

Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in complex with an H7 SH13 HA trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: V.10, N.28 Chain C: N.33, G.34 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.10 Hydrogen bonds: C:N.33 NAG.2: 5 residues within 4Å: Chain B: E.72, K.75, G.78, N.79, N.82 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.75 Hydrogen bonds: B:E.72, B:N.82 NAG.3: 4 residues within 4Å: Chain B: D.147, A.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.154, B:T.156 NAG.4: 5 residues within 4Å: Chain E: E.72, K.75, G.78, N.79, N.82 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.75 Hydrogen bonds: E:E.72, E:N.82 NAG.5: 4 residues within 4Å: Chain E: D.147, A.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.154, E:T.156 NAG.6: 5 residues within 4Å: Chain H: E.72, K.75, G.78, N.79, N.82 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:K.75 Hydrogen bonds: H:E.72, H:N.82 NAG.7: 4 residues within 4Å: Chain H: D.147, A.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.154, H:T.156 NAG.8: 4 residues within 4Å: Chain F: N.33, G.34 Chain K: V.10, N.28 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain F Hydrophobic interactions: K:V.10 Hydrogen bonds: F:N.33 NAG.9: 4 residues within 4Å: Chain I: N.33, G.34 Chain L: V.10, N.28 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:N.33 Hydrophobic interactions: L:V.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheung, C.S. et al., Structure of an influenza group 2-neutralizing antibody targeting the hemagglutinin stem supersite. Structure (2022)

Release Date

2021-06-09

Peptides

Hemagglutinin HA1 chain: AKL
Hemagglutinin HA2 chain: BEH
1D12 Light chain: CFI
1D21 Heavy chain: DGJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
C

L
G

B
B

E
D

H
I

C
L

F
E

I
J

D
H

G
F

J
K

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

1D12 Light chain

1D21 Heavy chain