SMTL ID : 8sav.1

CryoEM structure of VRC01-CH848.0526.25

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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: 9 residues within 4Å: Chain I: K.314, N.317, E.318, Q.321, N.373, G.374, T.375, D.376, I.377 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.317, I:D.376, I:E.318, I:Q.321 NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: R.340, A.349, N.363, S.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.340, A:R.340 NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: Y.112, R.115, T.276, Q.306, H.308, N.310, T.386, T.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.306 NAG-NAG-BMA.6: 10 residues within 4Å: Chain A: K.314, N.317, E.318, Q.321, Y.372, N.373, G.374, T.375, D.376, I.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.317, A:D.376, A:E.318, A:Q.321 NAG-NAG-BMA.7: 4 residues within 4Å: Chain E: R.340, A.349, N.363, S.365 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.340, E:R.340 NAG-NAG-BMA.8: 8 residues within 4Å: Chain E: Y.112, D.113, R.115, T.276, H.308, N.310, T.386, T.388 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 10 residues within 4Å: Chain E: K.314, N.317, E.318, Q.321, Y.372, N.373, G.374, T.375, D.376, I.377 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.317, E:D.376, E:E.318, E:Q.321 NAG-NAG-BMA.12: 4 residues within 4Å: Chain I: R.340, A.349, N.363, S.365 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.340, I:R.340 NAG-NAG-BMA.13: 8 residues within 4Å: Chain I: Y.112, R.115, T.276, Q.306, H.308, N.310, T.386, T.388 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.306

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.4: 5 residues within 4Å: Chain A: A.104, T.105, N.133, Y.150, D.299 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.150 NAG-NAG.9: 5 residues within 4Å: Chain E: A.104, T.105, N.133, Y.150, D.299 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain I: A.104, T.105, N.133, Y.150, D.299 No protein-ligand interaction detected (PLIP)

3 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.5: 7 residues within 4Å: Chain A: E.190, L.240, N.241, N.354, G.356, K.419, S.420 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.190, A:G.356 NAG-NAG-BMA-MAN-MAN.10: 8 residues within 4Å: Chain E: T.188, E.190, L.240, N.241, N.354, G.356, K.419, S.420 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.190, E:G.356 NAG-NAG-BMA-MAN-MAN.15: 7 residues within 4Å: Chain I: E.190, L.240, N.241, N.354, G.356, K.419, S.420 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:E.190, I:G.356

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

NAG.16: 2 residues within 4Å: Chain A: V.106, N.108 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain A: N.369, D.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.369, A:D.376 NAG.18: 2 residues within 4Å: Chain E: V.106, N.108 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain E: N.369, D.376 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.369, E:D.376 NAG.20: 2 residues within 4Å: Chain I: V.106, N.108 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain I: N.369, D.376 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.369, I:D.376

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

CH848.0526.25 gp120: AEI
CH848.0526.25 gp41: BFJ
VRC01 variable heavy chain: CGK
VRC01 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

CH848.0526.25 gp120

CH848.0526.25 gp41

VRC01 variable heavy chain

VRC01 variable light chain

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