SMTL ID : 9dwe.1

Cryo-EM structure of hemagglutinin H5 A/Texas/37/2024 in complex with LSTa and antibody CR9114

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.1: 15 residues within 4Å: Chain F: Y.107, L.145, G.146, V.147, S.148, A.149, W.165, I.167, H.195, E.202, L.206, G.237, Q.238, R.239, G.240 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Q.238, F:R.239, F:G.240, F:V.147, F:A.149, F:Q.238, F:G.240 Hydrophobic interactions: F:W.165, F:I.167 GAL-SIA.2: 15 residues within 4Å: Chain I: Y.107, L.145, G.146, V.147, S.148, A.149, W.165, I.167, H.195, E.202, L.206, G.237, Q.238, R.239, G.240 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:Q.238, I:R.239, I:V.147, I:A.149, I:Q.238, I:Q.238, I:G.240 Hydrophobic interactions: I:W.165, I:I.167 GAL-SIA.3: 14 residues within 4Å: Chain C: Y.107, L.145, G.146, V.147, S.148, A.149, W.165, I.167, H.195, E.202, L.206, Q.238, R.239, G.240 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.238, C:R.239, C:G.240, C:V.147, C:A.149, C:Q.238, C:Q.238 Hydrophobic interactions: C:W.165, C:I.167

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

NAG.4: 3 residues within 4Å: Chain C: N.26, N.27, Q.360 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain C: Q.31, K.38, N.39 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain C: N.181, D.252, A.254, H.256 Chain I: S.233 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain C: N.54, N.291, N.302 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain C: E.495, N.499, T.501 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain F: N.27, P.337, Q.360 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain F: K.38, N.39 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain C: S.233, R.239 Chain F: N.181, A.254, H.256 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain F: N.54, C.58, A.300, N.302 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain F: E.492, E.495, N.499, T.501 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain I: N.26, N.27, Q.360 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain I: Q.31, K.38, N.39 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain F: S.233 Chain I: N.181, A.254 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain I: N.54, C.58, A.300, N.302 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain I: E.495, S.496, N.499, T.501 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Good, M.R. et al., A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth. Nat Commun (2024)

Release Date

2024-12-04

Peptides

CR9114 Fab light chain: ADG
CR9114 Fab Fab heavy chain: BEH
Hemagglutinin: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

D
M

G
N

B
H

E
I

H
J

C
A

F
B

I
C

CR9114 Fab light chain

CR9114 Fab Fab heavy chain

Hemagglutinin