SMTL ID : 7ugn.1

Cryo-EM structure of BG24 inferred germline Fabs with germline CDR3s and 10-1074 Fabs in complex with HIV-1 Env immunogen BG505-SOSIPv4.1-GT1 - Class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

18 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 5 residues within 4Å: Chain A: T.102, N.114, H.131, L.133, D.279 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.193, T.195, S.233 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: Q.252, N.254, S.292, R.389 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.260, I.281 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.321, D.344, S.346 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: L.224, N.393 Ligands: NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: T.102, N.114, H.131, L.133, D.279 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.193, T.195, S.233 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: Q.252, N.254, S.292, R.389 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.260, I.281 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.321, D.344, S.346 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: L.224, N.393 Ligands: NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: T.102, N.114, L.133, D.279 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.193, T.195, S.233 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain C: Q.252, N.254, V.291, S.292, S.358, R.389 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: N.260, I.281 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.321, D.344, S.346 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain C: N.221, P.250, N.393 Ligands: NAG-NAG-BMA-MAN-MAN.19 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.3: 7 residues within 4Å: Chain A: L.220, N.221, N.335, G.337, V.391, S.392 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.337 NAG-NAG-BMA-MAN-MAN.11: 7 residues within 4Å: Chain B: L.220, N.221, N.335, G.337, V.391, S.392 Ligands: NAG-NAG.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.337 NAG-NAG-BMA-MAN-MAN.19: 7 residues within 4Å: Chain C: L.220, N.221, N.335, G.337, V.391, S.392 Ligands: NAG-NAG.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.337

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.6: 14 residues within 4Å: Chain A: T.256, H.288, N.290, R.389 Chain M: R.103, I.104, G.106, V.107, V.108 Chain P: N.43, N.44, Q.45, D.60, I.61 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN.22: 13 residues within 4Å: Chain C: T.256, H.288, N.290 Chain O: R.103, I.104, G.106, V.107, V.108 Chain R: N.43, N.44, Q.45, D.60, I.61 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:V.108

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.14: 12 residues within 4Å: Chain B: T.256, H.288, N.290, R.389 Chain N: R.103, I.104, G.106, V.107, V.108 Chain Q: D.60, I.61 Ligands: MAN.40 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:V.108, N:R.103

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

NAG.25: 1 residues within 4Å: Chain A: N.55 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.100, D.106, K.113 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: Q.97, S.116, F.117, N.118 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: S.346, N.350 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.55 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.100, D.106, K.113 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: Q.97, S.116, F.117, N.118 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: S.346, N.350 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.54, N.55 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.100, D.106, K.113 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: Q.97, S.116, F.117, N.118 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: S.346, N.350 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: N.102, Y.103 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain E: N.102, Y.103 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.102, Y.103 Ligand excluded by PLIP

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.40: 7 residues within 4Å: Chain N: R.103 Chain Q: N.43, N.44, Q.45, D.60 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN.14 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain N Hydrogen bonds: Q:N.43, Q:D.60, N:R.103

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

2022-10-26

Peptides

Envelope glycoprotein gp120: ABC
Envelope glycoprotein gp41: DEF
BG24 inferred germline Fab with germline CDR3s heavy chain: GHI
BG24 inferred germline Fab with germline CDR3s 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 inferred germline Fab with germline CDR3s heavy chain

BG24 inferred germline Fab with germline CDR3s light chain

10-1074 Fab heavy chain

10-1074 Fab light chain

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