SMTL ID : 8saz.1

CryoEM structure of DH270.I5.6-CH848.10.17

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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.1: 9 residues within 4Å: Chain E: N.263, T.265 Chain G: Q.62 Chain H: A.3, Y.27, Y.32, A.94, G.95, S.96 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.27, H:A.94, H:S.96 NAG-NAG-BMA-MAN-MAN.5: 9 residues within 4Å: Chain I: N.263, T.265 Chain K: Q.62 Chain L: A.3, Y.27, Y.32, A.94, G.95, S.96 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Y.27, L:A.94, L:S.96

3 x NAG- NAG- BMA- 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-(1-6)-[alpha-D-mannopyranose-(1-3)]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.2: 20 residues within 4Å: Chain E: H.291, N.293, T.371, T.373 Chain G: T.28, D.31, Y.32, R.98, W.101, Y.106, N.113, D.115, Y.116 Chain H: L.48, Y.51, E.52, K.55, R.56, P.57, S.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7: 19 residues within 4Å: Chain I: H.291, N.293, T.371, T.373 Chain K: T.28, D.31, Y.32, R.98, W.101, Y.106, N.113, D.115, Y.116 Chain L: L.48, Y.51, E.52, K.55, P.57, S.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10: 20 residues within 4Å: Chain A: H.291, N.293, T.371, T.373 Chain C: T.28, D.31, Y.32, R.98, W.101, Y.106, N.113, D.115, Y.116 Chain D: L.48, Y.51, E.52, K.55, R.56, P.57, S.58 No protein-ligand interaction detected (PLIP)

4 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.3: 4 residues within 4Å: Chain E: N.116, E.132, Y.133, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.6: 4 residues within 4Å: Chain I: N.116, K.131, Y.133, D.282 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:K.131, I:Y.133 NAG-NAG-BMA-MAN.9: 8 residues within 4Å: Chain A: N.263, T.265 Chain D: A.3, Y.27, Y.32, A.94, G.95, S.96 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.27, D:A.94, D:S.96 NAG-NAG-BMA-MAN.11: 4 residues within 4Å: Chain A: N.116, K.131, Y.133, D.282 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.131

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.4: 4 residues within 4Å: Chain E: N.400, I.401, T.402, R.404 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.404, E:R.404 NAG-NAG-BMA.8: 4 residues within 4Å: Chain I: N.400, I.401, T.402, R.404 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.404, I:R.404 NAG-NAG-BMA.12: 4 residues within 4Å: Chain A: N.400, I.401, T.402, R.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.404, A: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

Envelope glycoprotein gp160: AEI
CH848.10.17.SOSIP gp41: BFJ
DH270.I5.6 variable heavy chain: CGK
DH270.I5.6 variable light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
K

B
B

F
F

J
L

C
C

G
H

K
M

D
D

H
I

L
N

Envelope glycoprotein gp160

CH848.10.17.SOSIP gp41

DH270.I5.6 variable heavy chain

DH270.I5.6 variable light chain

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