SMTL ID : 6um7.1

Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex with CH848 10.17DT Env

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

12 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: 6 residues within 4Å: Chain A: N.224, N.337, C.338, C.403, R.404, S.405 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 8 residues within 4Å: Chain A: N.263, I.284 Chain D: T.44, Y.46, D.47, Y.51, Y.112, S.115 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.47 NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: N.116, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: Q.323, S.348, N.349, N.352 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 6 residues within 4Å: Chain F: N.224, N.337, C.338, C.403, R.404, S.405 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 8 residues within 4Å: Chain F: N.263, I.284 Chain H: T.44, Y.46, D.47, Y.51, Y.112, S.115 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.47 NAG-NAG-BMA.9: 2 residues within 4Å: Chain F: N.116, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain F: Q.323, S.348, N.349, N.352 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 6 residues within 4Å: Chain L: N.224, N.337, C.338, C.403, R.404, S.405 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 8 residues within 4Å: Chain K: T.44, Y.46, D.47, Y.51, Y.112, S.115 Chain L: N.263, I.284 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.47 NAG-NAG-BMA.14: 2 residues within 4Å: Chain L: N.116, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain L: Q.323, S.348, N.349, N.352 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.3: 10 residues within 4Å: Chain A: H.291, N.293, T.371, T.373 Chain C: W.120, Y.124, Y.125, Y.130, N.134 Chain D: Y.70 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.8: 10 residues within 4Å: Chain F: H.291, N.293, T.371, T.373 Chain G: W.120, Y.124, Y.125, Y.130, N.134 Chain H: Y.70 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.13: 10 residues within 4Å: Chain J: W.120, Y.124, Y.125, Y.130, N.134 Chain K: Y.70 Chain L: H.291, N.293, T.371, T.373 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: N.346, R.377 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: K.320, Y.321, N.322, R.427 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: R.154, N.159 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: T.98, N.120 Chain F: D.127 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: N.196, T.198, S.236, E.237, N.238, L.239 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: G.57, N.58 Chain B: G.24, S.25 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: V.55, N.191, N.203, S.205 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: N.300, L.303, G.353, T.354, Y.355 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain F: N.346, R.377 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain F: K.320, Y.321, N.322, R.427 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain F: R.154, N.159 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain F: T.98, N.120 Chain L: D.127 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain F: N.196, T.198, S.236, E.237, N.238, L.239 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain E: G.24, S.25 Chain F: G.57, N.58 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain F: V.55, N.191, N.203, S.205 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain F: N.300, L.303, G.353, T.354, Y.355 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain L: N.346, R.377 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain L: K.320, Y.321, N.322, R.427 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain L: R.154, N.159 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: D.127 Chain L: T.98, N.120 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain L: N.196, T.198, S.236, E.237, N.238, L.239 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain I: G.24, S.25 Chain L: G.57, N.58 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain L: V.55, N.191, N.203, S.205 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain L: N.300, L.303, G.353, T.354, Y.355 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saunders, K.O. et al., Targeted selection of HIV-specific antibody mutations by engineering B cell maturation. Science (2019)

Release Date

2019-12-18

Peptides

Envelope glycoprotein gp120: AFL
Envelope glycoprotein gp41: BEI
DH270.mu1 Fab Heavy Chain: CGJ
DH270.mu1 Fab Light chain: DHK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
E

L
I

B
H

E
D

I
1

C
J

G
F

J
B

D
K

H
G

K
C

Envelope glycoprotein gp120

Envelope glycoprotein gp41

DH270.mu1 Fab Heavy Chain

DH270.mu1 Fab Light chain

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