SMTL ID : 8san.1

CryoEM structure of VRC01-CH848.0836.10

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-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: 3 residues within 4Å: Chain A: V.142, R.155, N.160 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.142 NAG-NAG-BMA.4: 3 residues within 4Å: Chain E: V.142, R.155, N.160 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.142 NAG-NAG-BMA.7: 5 residues within 4Å: Chain I: V.142, R.155, I.157, N.160 Chain K: D.73 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.142

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.2: 12 residues within 4Å: Chain A: K.33, E.34, T.172, E.174, V.217, L.224, N.225, R.267, N.338, G.340, K.405, S.406 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.340, A:K.405 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 12 residues within 4Å: Chain E: K.33, E.34, T.172, E.174, P.175, V.217, N.225, R.267, N.338, G.340, K.405, S.406 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.340 NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 13 residues within 4Å: Chain C: Q.1 Chain I: Y.31, K.33, E.34, T.172, E.174, N.225, R.267, F.337, N.338, G.340, K.405, S.406 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.340

3 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.3: 7 residues within 4Å: Chain A: N.239 Chain C: Y.104 Chain D: Y.28, R.64, W.65, G.66, P.67 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.28 Hydrogen bonds: D:R.64, D:R.64, D:R.64, D:G.66 NAG-NAG-BMA-MAN-MAN-MAN.6: 6 residues within 4Å: Chain E: N.239 Chain H: Y.28, R.64, W.65, G.66, P.67 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.28 Hydrogen bonds: H:R.64, H:R.64, H:G.66 NAG-NAG-BMA-MAN-MAN-MAN.9: 8 residues within 4Å: Chain I: N.239, T.241, N.242 Chain L: Y.28, R.64, W.65, G.66, P.67 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:Y.28 Hydrogen bonds: L:R.64, L:R.64, L:G.66

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

CH848.0836.10 gp120: AEI
CH848.0836.10 gp41: BFJ
VCR01 variable heavy chain: CGK
VCR01 variable light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

CH848.0836.10 gp120

CH848.0836.10 gp41

VCR01 variable heavy chain

VCR01 variable light chain

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