SMTL ID : 7ugq.1

Cryo-EM structure of BG24 Fabs with an inferred germline CDRL1 and 10-1074 Fabs in complex with HIV-1 Env 6405-SOSIP.664

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-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: 5 residues within 4Å: Chain A: K.100, N.107, H.124, V.266, I.267 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: N.185, P.189, S.225, L.228, L.297 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 7 residues within 4Å: Chain A: A.400, D.401, S.404, N.406 Chain G: Q.62, R.63, R.67 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.63, G:R.67, G:Q.62 NAG-NAG-BMA.13: 5 residues within 4Å: Chain B: K.100, N.107, H.124, V.266, I.267 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 5 residues within 4Å: Chain B: N.185, T.187, S.225, L.228, L.297 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 10 residues within 4Å: Chain B: R.300, G.399, A.400, D.401, S.404, N.406, E.407 Chain H: Q.62, R.63, R.67 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.63, H:R.67 NAG-NAG-BMA.25: 5 residues within 4Å: Chain C: K.100, N.107, H.124, V.266, I.267 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 4 residues within 4Å: Chain C: N.185, T.187, S.225, L.228 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 6 residues within 4Å: Chain C: S.404, N.406, T.408 Chain I: Q.62, R.63, R.67 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.63, I:R.67, I:Q.62

21 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: Q.95, S.109, N.111, K.122 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: E.133, I.135, M.143, N.148 Chain C: V.115 Chain G: D.73 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.246, N.277, S.279, I.353 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain A: N.59, T.187, N.227 Chain G: A.106 Chain J: Y.31, Y.33, F.92 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.187 Hydrogen bonds: A:N.59 NAG-NAG.8: 4 residues within 4Å: Chain A: D.282, N.285, S.346, N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: D.220, I.221, N.240, W.289, T.292 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.292 NAG-NAG.10: 5 residues within 4Å: Chain A: T.316, T.317, N.330, Q.357 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: Q.95, S.109, N.111, K.122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain A: V.115 Chain B: E.133, I.135, M.143, N.148 Chain H: D.73 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain B: N.246, N.277, S.279, I.353, S.386 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain B: N.59, T.187, E.226, N.227 Chain H: A.106 Chain K: Y.31, Y.33, F.92 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.187 NAG-NAG.20: 4 residues within 4Å: Chain B: D.282, N.285, S.346, N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain B: D.220, I.221, N.240, W.289 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.289 NAG-NAG.22: 6 residues within 4Å: Chain B: T.316, T.317, N.330, S.332, Q.357 Ligands: NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: Q.95, S.109, N.111, K.122 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 6 residues within 4Å: Chain B: V.115 Chain C: E.133, I.135, M.143, N.148 Chain I: D.73 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain C: N.246, N.277, S.279, I.353 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 8 residues within 4Å: Chain C: N.59, T.187, E.226, N.227 Chain I: A.106 Chain L: Y.31, Y.33, F.92 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.187 NAG-NAG.32: 3 residues within 4Å: Chain C: D.282, N.285, N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 6 residues within 4Å: Chain C: D.220, I.221, N.240, Q.288, W.289, T.292 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.288, C:T.292 NAG-NAG.34: 6 residues within 4Å: Chain C: T.316, T.317, N.330, S.332, Q.357 Ligands: NAG.55 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: 13 residues within 4Å: Chain A: T.160, E.162, V.205, L.212, N.213, F.320, T.321, G.323, I.379, S.386, S.387 Chain H: Q.1 Ligands: NAG.42 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain H Hydrogen bonds: A:G.323, A:S.386, H:Q.1 NAG-NAG-BMA-MAN-MAN.17: 12 residues within 4Å: Chain B: T.160, E.162, V.205, L.212, N.213, F.320, T.321, G.323, S.386, S.387 Chain I: Q.1 Ligands: NAG.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.323, B:S.386 NAG-NAG-BMA-MAN-MAN.29: 11 residues within 4Å: Chain C: T.160, E.162, L.212, N.213, F.320, T.321, G.323, S.386, S.387 Chain G: Q.1 Ligands: NAG.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.323, C:S.386

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.12: 19 residues within 4Å: Chain A: N.246, T.248, R.272, H.275, N.277, I.353 Chain M: Q.102, R.103, I.104, Y.105, G.106, V.107, V.108 Chain P: S.23, N.43, Q.45, P.59, D.60, I.61 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:Y.105, M:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.36: 20 residues within 4Å: Chain C: T.248, R.272, H.275, N.277, I.353, L.384 Chain O: Q.102, R.103, I.104, Y.105, G.106, V.107, V.108 Chain R: S.23, N.43, N.44, Q.45, P.59, D.60, I.61 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:Y.105, O:V.108

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.24: 20 residues within 4Å: Chain B: T.248, R.272, H.275, N.277, I.353 Chain N: Q.102, R.103, I.104, Y.105, G.106, V.107, V.108, Y.116 Chain Q: S.23, N.43, N.44, Q.45, P.59, D.60, N.62 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:Y.105, N:V.108, N:Q.102

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

NAG.37: 2 residues within 4Å: Chain A: V.52, N.53 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: E.50, N.192 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.252 Chain P: N.62 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: N.299, H.405 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: G.333, N.336 Ligands: NAG-NAG.10 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain A: L.216, S.242, S.386, N.388 Ligands: NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain A: D.401, N.402, S.403 Chain J: A.2, T.4 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: V.52, N.53 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.192 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.252 Chain Q: N.62 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.299, H.405 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: G.333, N.336 Ligands: NAG-NAG.22 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain B: N.402 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain B: L.216, S.242, S.386, N.388 Ligands: NAG-NAG-BMA-MAN-MAN.17 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: V.52, N.53 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: E.50, N.192 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.252 Chain R: N.62 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.299, H.405 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: G.333, N.336 Ligands: NAG-NAG.34 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.402, S.403 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain C: L.216, S.242, S.386, N.388 Ligands: NAG-NAG-BMA-MAN-MAN.29 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain D: N.102 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain E: N.102 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain F: N.102 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
BG24 with an inferred germline CDRL1 Fab heavy chain: GHI
BG24 with an inferred germline CDRL1 Fab light chain: JKL
10-1074 Fab heavy chain: MNO
10-1074 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
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

Envelope glycoprotein gp120

Envelope glycoprotein gp41

BG24 with an inferred germline CDRL1 Fab heavy chain

BG24 with an inferred germline CDRL1 Fab light chain

10-1074 Fab heavy chain

10-1074 Fab light chain

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