SMTL ID : 7ugo.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x NAG- NAG- BMA- MAN: 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.1: 9 residues within 4Å: Chain A: V.216, L.223, N.224, N.338, G.340, V.406, S.407 Ligands: NAG.23, MAN.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.340 NAG-NAG-BMA-MAN.15: 10 residues within 4Å: Chain C: E.173, V.216, L.223, N.224, N.338, G.340, V.406, S.407 Ligands: NAG.38, MAN.41 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.173, C:G.340

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)]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.2: 7 residues within 4Å: Chain A: T.259, H.291, N.293 Chain G: I.104, G.106, V.108 Ligands: MAN-MAN.6 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.108

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

NAG-NAG.3: 2 residues within 4Å: Chain A: N.263, V.402 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: Q.255, N.257, S.295, R.404 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: V.103, N.117, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.263, V.402 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: Q.255, N.257, S.295, R.404 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: V.103, N.117 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: N.263, V.402 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: Q.255, N.257, S.295, R.404 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain C: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: V.103, N.117, D.282 No protein-ligand interaction detected (PLIP)

2 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.6: 6 residues within 4Å: Chain G: R.103 Chain J: N.43, Q.45, D.60, I.61 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.2 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:N.43, J:Q.45, J:Q.45, J:D.60 MAN-MAN.13: 8 residues within 4Å: Chain H: R.103, I.104, Y.105 Chain K: N.43, Q.45, D.60, I.61 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.9 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain H Hydrogen bonds: K:N.43, K:N.43, K:Q.45, H:R.103

1 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.8: 11 residues within 4Å: Chain B: E.173, V.216, L.223, N.224, N.338, G.340, V.406, S.407 Ligands: MAN.28, NAG.31, MAN.35 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.173, B:G.340

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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.9: 7 residues within 4Å: Chain B: T.259, H.291, N.293 Chain H: I.104, G.106 Ligands: MAN-MAN.13, MAN-MAN.13 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN.16: 10 residues within 4Å: Chain C: T.259, H.291, N.293 Chain I: R.103, I.104, G.106 Chain L: N.43, Q.45, D.60, I.61 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:N.43, L:Q.45, L:D.60

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

NAG.21: 1 residues within 4Å: Chain A: N.57 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.196, T.198, S.236 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.224, P.253, N.408 Ligands: NAG-NAG-BMA-MAN.1 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: S.349, N.353 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.121, K.132 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.102 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.57 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.196, T.198, S.236 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.224, P.253, N.408 Ligands: NAG-NAG-BMA.8 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: S.349, N.353 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.121, K.132 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.102 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.57 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.196, T.198, S.236 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.224, P.253, N.408 Ligands: NAG-NAG-BMA-MAN.15 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: S.349, N.353 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.102 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: D.128 Chain C: Q.99, N.121 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain D: K.98, E.99, N.102 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: K.98, N.102 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain F: K.98, E.99, N.102 Ligand excluded by PLIP

4 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.27: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) MAN.28: 1 residues within 4Å: Ligands: NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP) MAN.35: 1 residues within 4Å: Ligands: NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP) MAN.41: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.15 No protein-ligand interaction detected (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

2022-10-26

Peptides

Envelope glycoprotein gp120: ABC
Envelope glycoprotein gp41: DEF
10-1074 Fab heavy chain: GHI
10-1074 Fab light chain: JKL
BG24 inferred germline Fab with mature CDR3s heavy chain: MNO
BG24 inferred germline Fab with mature CDR3s 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
P

K
Q

L
R

M
G

N
H

O
I

P
J

Q
K

R
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

10-1074 Fab heavy chain

10-1074 Fab light chain

BG24 inferred germline Fab with mature CDR3s heavy chain

BG24 inferred germline Fab with mature CDR3s light chain

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