SMTL ID : 7ll2.1

Cryo-EM structure of BG505 DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody VRC33.01 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

21 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: E.57, N.58 Chain B: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: V.104, T.105, N.118, Y.135, L.137, G.289, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: R.162, N.167 Chain I: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.9, NAG-NAG-BMA-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 1 residues within 4Å: Chain A: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain E: E.57, N.58 Chain F: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 6 residues within 4Å: Chain E: V.104, T.105, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 2 residues within 4Å: Chain E: T.98, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 3 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain E: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.20, NAG-NAG-BMA-MAN-MAN.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 1 residues within 4Å: Chain E: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain I: E.57, N.58 Chain J: G.13, S.17, T.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 5 residues within 4Å: Chain I: T.105, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 2 residues within 4Å: Chain I: T.98, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 3 residues within 4Å: Chain E: R.278 Chain I: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 4 residues within 4Å: Chain I: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 4 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 1 residues within 4Å: Chain I: N.361 No protein-ligand interaction detected (PLIP)

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.2: 4 residues within 4Å: Chain A: C.101, T.102, N.103, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain E: N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain I: C.101, T.102, N.103, Y.161 No protein-ligand interaction detected (PLIP)

6 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.7: 8 residues within 4Å: Chain A: E.181, L.231, N.232, N.346, C.413, V.414, S.415 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.414 NAG-NAG-BMA-MAN-MAN.9: 6 residues within 4Å: Chain A: N.332, S.333, N.355, S.357 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.18: 7 residues within 4Å: Chain E: L.231, N.232, N.346, C.413, V.414, S.415 Ligands: NAG.40 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.414 NAG-NAG-BMA-MAN-MAN.20: 6 residues within 4Å: Chain E: N.332, S.333, N.355, S.357 Ligands: NAG-NAG-BMA.21, NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.29: 8 residues within 4Å: Chain I: E.181, L.231, N.232, N.346, C.413, V.414, S.415 Ligands: NAG.44 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:V.414 NAG-NAG-BMA-MAN-MAN.31: 5 residues within 4Å: Chain I: N.332, S.333, N.355, S.357 Ligands: NAG-NAG-BMA.32 No protein-ligand interaction detected (PLIP)

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.8: 12 residues within 4Å: Chain A: N.246, N.249 Chain C: E.50, Y.58, K.99, S.104, Y.105, N.107 Chain D: Y.95, A.97, D.98, P.99 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.105 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 12 residues within 4Å: Chain E: N.246, N.249 Chain G: E.50, Y.58, K.99, S.104, Y.105, N.107 Chain H: Y.95, A.97, D.98, P.99 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.105 NAG-NAG-BMA-MAN-MAN-MAN-MAN.30: 13 residues within 4Å: Chain I: N.246, N.249 Chain K: E.50, Y.58, K.99, S.104, Y.105, N.107 Chain L: Y.95, M.96, A.97, D.98, P.99 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:Y.105

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

NAG.34: 4 residues within 4Å: Chain A: Q.263, N.265, S.303, R.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.263, A:Q.263, A:R.412, A:R.412 NAG.35: 3 residues within 4Å: Chain A: N.271, I.292, V.410 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.410 Hydrogen bonds: A:N.271 NAG.36: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG.37: 1 residues within 4Å: Chain A: N.324 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.324 NAG.38: 4 residues within 4Å: Chain E: Q.263, N.265, S.303, R.412 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.263, E:Q.263, E:R.412, E:R.412 NAG.39: 3 residues within 4Å: Chain E: N.271, I.292, V.410 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.410 NAG.40: 3 residues within 4Å: Chain E: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG.41: 1 residues within 4Å: Chain E: N.324 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.324 NAG.42: 4 residues within 4Å: Chain I: Q.263, N.265, S.303, R.412 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:Q.263, I:Q.263, I:R.412, I:R.412 NAG.43: 3 residues within 4Å: Chain I: N.271, I.292, V.410 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:V.410 Hydrogen bonds: I:N.271 NAG.44: 3 residues within 4Å: Chain I: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.29 No protein-ligand interaction detected (PLIP) NAG.45: 1 residues within 4Å: Chain I: N.324 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.324

Links

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Citation

Cottrell, C.A. et al., Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Cell Rep (2021)

Release Date

2021-03-17

Peptides

Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
VRC33.01 Fab Heavy chain: CGK
VRC33.01 Fab Light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
E

B
B

F
D

J
F

C
H

G
I

K
K

D
L

H
J

L
M

Envelope glycoprotein gp120

Envelope glycoprotein gp41

VRC33.01 Fab Heavy chain

VRC33.01 Fab Light chain

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