SMTL ID : 8f38.1

Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain E: N.71, N.81, E.83, E.103, N.104, C.107, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain F: N.71, N.81, E.83, E.103, N.104, C.107, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 7 residues within 4Å: Chain G: N.71, N.81, E.83, E.103, N.104, C.107, R.237 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 1 residues within 4Å: Chain E: N.40 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain F: N.40 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain G: N.40 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain E: N.28 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain E: N.142 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain E: N.55, C.291, D.292, N.303 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain E: E.490, N.497, T.499 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain E: N.71 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain E: N.176 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain F: N.28 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain F: P.141, N.142 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain F: N.55, C.291, D.292, N.303 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain F: E.490, N.497, T.499 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain F: N.71 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain F: N.176 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain G: P.141, N.142 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain G: N.55, C.291, D.292, N.303 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain G: E.490, S.494, N.497, T.499 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain G: N.71 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain G: N.176 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain G: N.28 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagashima, K.A. et al., Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6. Structure (2024)

Release Date

2023-12-13

Peptides

CR6261 Fab light chain: AHI
CR6261 Fab heavy chain: BCD
hemagglutinin: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

H
H

I
I

B
D

C
E

D
F

E
A

F
B

G
C

CR6261 Fab light chain

CR6261 Fab heavy chain

hemagglutinin

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