SMTL ID : 8vef.1

Cryo-EM structure of antibody T5-1E08 UCA (unmutated common ancestor) in complex with stabilized H1N1 Influenza Hemagglutinin Trimer (A/Kiev/1/57)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG.1: 7 residues within 4Å: Chain A: N.81, E.83, E.103, N.104, C.107, P.153, R.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.237 NAG-NAG.2: 5 residues within 4Å: Chain A: N.90, E.129, R.130, F.131, Q.185 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: E.490, E.493, S.494, N.497, T.499 Chain C: Y.94 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.94 NAG-NAG.5: 7 residues within 4Å: Chain D: N.81, E.83, E.103, N.104, C.107, P.153, R.237 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.237 NAG-NAG.6: 5 residues within 4Å: Chain D: N.90, E.129, R.130, F.131, Q.185 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain D: E.490, E.493, S.494, N.497, T.499 Chain F: Y.94 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.94 NAG-NAG.9: 7 residues within 4Å: Chain G: N.81, E.83, E.103, N.104, C.107, P.153, R.237 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.237 NAG-NAG.11: 6 residues within 4Å: Chain G: E.490, E.493, S.494, N.497, T.499 Chain I: Y.94 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Y.94

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.3: 4 residues within 4Å: Chain A: N.176 Chain G: E.202, R.205, D.211 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.205, G:R.205, G:R.205, G:E.202, G:E.202 NAG-NAG-BMA-MAN-MAN-MAN.7: 5 residues within 4Å: Chain A: E.202, R.205, R.209, D.211 Chain D: N.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.205, A:R.205, A:R.205, A:E.202, A:E.202 NAG-NAG-BMA-MAN-MAN-MAN.10: 5 residues within 4Å: Chain D: E.202, R.205, D.211 Chain G: N.176, Y.214 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.205, D:R.205, D:R.205, D:E.202, D:E.202

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.12: 1 residues within 4Å: Chain A: N.28 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain A: N.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40 NAG.14: 1 residues within 4Å: Chain D: N.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.28 NAG.15: 1 residues within 4Å: Chain D: N.40 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.40 NAG.16: 1 residues within 4Å: Chain G: N.28 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.28 NAG.17: 1 residues within 4Å: Chain G: N.40 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.40 NAG.18: 3 residues within 4Å: Chain G: N.90, E.129, R.130 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mantus, G.E. et al., Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages. Structure (2025)

Release Date

2025-03-19

Peptides

Hemagglutinin: ADG
T5-1E08 UCA Fab heavy chain: BEH
T5-1E08 UCA Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

G
E

B
H

E
J

H
G

C
L

F
K

I
I

Hemagglutinin

T5-1E08 UCA Fab heavy chain

T5-1E08 UCA Fab light chain

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