SMTL ID : 7ugp.1

Cryo-EM structure of BG24 Fabs with an inferred germline light chain and 10-1074 Fabs in complex with HIV-1 Env immunogen BG505-SOSIPv4.1-GT1 containing the N276 gp120 glycan- Class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-[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.1: 18 residues within 4Å: Chain A: T.248, H.280, N.282, S.350, R.381 Chain G: R.103, I.104, Y.105, G.106, V.107, V.108 Chain M: S.23, N.43, N.44, Q.45, P.59, D.60, I.61 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.108 NAG-NAG-BMA-MAN-MAN-MAN.4: 17 residues within 4Å: Chain B: T.248, H.280, N.282, S.350, R.381 Chain H: R.103, I.104, Y.105, G.106, V.107, V.108 Chain N: S.23, N.43, N.44, Q.45, D.60, I.61 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:V.108 NAG-NAG-BMA-MAN-MAN-MAN.8: 18 residues within 4Å: Chain C: T.248, H.280, N.282, S.350, R.381 Chain I: R.103, I.104, Y.105, G.106, V.107, V.108 Chain O: S.23, N.43, N.44, Q.45, P.59, D.60, I.61 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.108

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: N.106, H.123, D.271 Chain M: R.90 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.106, L.125, D.271 Chain N: R.90 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: N.106, H.123, L.125, D.271 Chain O: R.90 No protein-ligand interaction detected (PLIP)

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.3: 8 residues within 4Å: Chain A: E.162, K.203, N.213, C.328, G.329, C.382, V.383 Ligands: NAG.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.162 Hydrogen bonds: A:G.329 NAG-NAG-BMA.6: 8 residues within 4Å: Chain B: E.162, K.203, N.213, C.328, G.329, V.383, S.384 Ligands: NAG.21 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.162 Hydrogen bonds: B:E.162, B:E.162, B:G.329 NAG-NAG-BMA.7: 10 residues within 4Å: Chain C: E.162, P.163, K.203, N.213, C.328, G.329, C.382, V.383, S.384 Ligands: NAG.42 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.162 Hydrogen bonds: C:G.329

33 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.10: 2 residues within 4Å: Chain A: N.51 Chain D: S.10 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: N.213, L.216, P.242, V.383, N.385 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.96, Q.138 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: T.187, E.226, N.227 Chain P: Y.31, N.32, Y.33 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.252, T.254, I.273, Q.377 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.342 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.313, S.314, S.315 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.185, T.187, S.225 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: Q.244, N.246, S.284, R.381 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: Q.93, N.110, R.119 Chain C: D.117 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: E.50, N.51 Chain E: S.10 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain B: N.213, L.216, P.242, V.383, N.385 Ligands: NAG-NAG-BMA.6 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.96, I.101 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain B: T.187, E.226, N.227 Chain Q: Y.31, N.32, Y.33 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.252, T.254, Q.377 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.342 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.313, S.314, S.315 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.185, T.187 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Q.244, N.246 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: Q.93, N.110, R.119 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: E.50, N.51 Chain F: S.10 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.96, K.128, N.139 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: T.187, E.226, N.227 Ligands: NAG.36 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.252, T.254, I.273 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.342 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.313, S.314, S.315 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain C: N.185, G.186, T.187, I.223, S.225 Ligands: NAG.32 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: Q.244, N.246, S.284 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Q.93, N.110, R.119 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: K.97, N.101 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: K.97, N.101 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain F: K.97, E.98, N.101 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: L.216, V.383, N.385 Ligands: NAG-NAG-BMA.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dam, K.A. et al., HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design. Nat Commun (2022)

Release Date

2022-11-09

Peptides

Envelope glycoprotein gp120: ABC
Envelope glycoprotein gp41: DEF
10-1074 Fab heavy chain: GHI
BG24 mature Fab heavy chain: JKL
10-1074 Fab light chain: MNO
BG24 mature Fab light chain: PQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
M

H
N

I
O

J
G

K
H

L
I

M
P

N
Q

O
R

P
J

Q
K

R
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

10-1074 Fab heavy chain

BG24 mature Fab heavy chain

10-1074 Fab light chain

BG24 mature Fab light chain

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