SMTL ID : 8sb2.1

CryoEM structure of DH270.I2-CH848.10.17

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

1 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: 5 residues within 4Å: Chain A: N.108 Chain C: T.58, V.68, T.69, R.84 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.84

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.2: 12 residues within 4Å: Chain A: N.263, I.284 Chain C: Q.62, Y.110 Chain D: Q.1, S.2, T.25, Y.27, Y.32, F.93, S.96, A.97 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.27, D:S.96, D:Q.1 NAG-NAG-BMA-MAN-MAN.12: 12 residues within 4Å: Chain I: N.263, I.284 Chain K: Q.62, Y.110 Chain L: Q.1, S.2, T.25, Y.27, Y.32, F.93, S.96, A.97 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Y.27, L:Q.1

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN-MAN.3: 22 residues within 4Å: Chain A: T.259, H.291, N.293, T.371, T.373 Chain C: G.26, D.31, F.32, G.99, W.101, S.103, Y.105, Y.106, Y.111, N.113, D.115 Chain D: Y.48, Y.51, E.52, R.56, P.57, S.58 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.26, C:D.31 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.8: 23 residues within 4Å: Chain E: T.259, H.291, N.293, T.371, T.373 Chain G: G.26, T.28, D.31, F.32, G.99, W.101, S.103, Y.105, Y.106, Y.111, N.113, D.115 Chain H: Y.48, Y.51, E.52, R.56, P.57, S.58 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.26, G:D.31 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13: 24 residues within 4Å: Chain I: T.259, H.291, N.293, T.371, T.373 Chain K: G.26, T.28, D.31, F.32, G.99, W.101, S.103, Y.105, Y.106, Y.111, N.113, D.115 Chain L: Y.48, Y.51, E.52, R.56, P.57, S.58 Ligands: NAG-NAG-BMA-MAN-MAN.15 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.26, K:T.28

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-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.4: 5 residues within 4Å: Chain A: A.104, T.105, N.116, Y.133, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.14: 7 residues within 4Å: Chain I: A.104, T.105, V.106, N.116, Y.133, D.282 Chain K: Q.65 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: 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.5: 4 residues within 4Å: Chain A: N.400, T.402 Chain C: Y.111 Chain D: Y.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.404 NAG-NAG-BMA-MAN.7: 10 residues within 4Å: Chain E: N.263, I.284 Chain G: Q.62, Y.110 Chain H: Y.27, Y.32, F.93, G.95, S.96, A.97 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.27, H:G.95

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.6: 4 residues within 4Å: Chain E: N.108 Chain G: T.58, T.69, R.84 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.84, G:R.84 NAG-NAG.10: 4 residues within 4Å: Chain E: N.400, T.402 Chain G: Y.111 Chain H: Y.32 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.404 NAG-NAG.11: 4 residues within 4Å: Chain I: N.108 Chain K: T.58, T.69, R.84 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.84, K:R.84

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-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.9: 6 residues within 4Å: Chain E: A.104, T.105, V.106, N.116, Y.133, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 6 residues within 4Å: Chain I: N.400, T.402 Chain L: Y.32 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henderson, R. et al., Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage. Nat Commun (2023)

Release Date

2023-04-19

Peptides

CH848.10.17.SOSIP gp120: AEI
CH848.10.17.SOSIP gp41: BFJ
DH270.I2.6 variable heavy chain: CGK
DH270.I2.6 variable light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
F

I
K

B
B

F
G

J
L

C
C

G
H

K
M

D
D

H
I

L
N

CH848.10.17.SOSIP gp120

CH848.10.17.SOSIP gp41

DH270.I2.6 variable heavy chain

DH270.I2.6 variable light chain

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