SMTL ID : 6vtt.1

Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.70 Å

Oligo State

hetero-3-1-1-3-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.98, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: A.102, K.103, N.117, Y.134 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: T.96, N.121, R.132 Chain D: W.109 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.194, P.202, N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: V.53, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.240, T.242, D.243 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: T.261, H.293, N.295 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: R.156, N.161 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.198, T.200, G.201 Ligands: NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.347, S.349, D.350, R.377 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.350 NAG-NAG.17: 3 residues within 4Å: Chain C: R.156, N.161, T.162 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.194, T.196 Ligands: NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: E.51, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain C: E.232, E.233, N.253, E.254, R.307, K.311 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain C: T.261, H.293, N.295, T.373 No protein-ligand interaction detected (PLIP)

2 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.4: 4 residues within 4Å: Chain A: V.143, R.156, N.161 Chain C: R.272 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 6 residues within 4Å: Chain C: T.96, S.119, N.121, K.130 Chain D: W.108, Q.118 No protein-ligand interaction detected (PLIP)

2 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: 7 residues within 4Å: Chain A: V.33, P.176, L.225, N.226, N.338, K.404, S.405 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 6 residues within 4Å: Chain C: K.103, N.117, Y.134, L.136 Chain D: E.104 Chain E: K.54 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.104, E:K.54

1 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.12: 12 residues within 4Å: Chain B: V.33, T.173, D.175, P.176, V.218, L.225, N.226, N.338, C.403, K.404, S.405 Ligands: NAG.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.175

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: 6 residues within 4Å: Chain C: N.98, R.132, E.154 Chain D: Q.26, F.27, R.28 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.26, D:F.27

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.20: 9 residues within 4Å: Chain C: P.170, P.176, V.218, L.225, N.226, N.338, K.404, S.405 Ligands: NAG.56 No protein-ligand interaction detected (PLIP)

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

NAG.23: 2 residues within 4Å: Chain A: E.55, N.56 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.198, T.200 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: E.233, N.253 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.265, I.286, G.399 Ligands: NAG.30 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.317 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain A: I.321, N.323, Q.324, N.354, K.355, R.427 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.347, D.350, R.377 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.400 Ligands: NAG.26 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.226, E.257, N.406 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: W.3, N.460 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: E.55, N.56 Chain H: S.18 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.98, E.154 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: K.103, N.117, Y.134 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.121, K.130, R.132 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.194, N.204 Ligands: NAG-NAG.11, NAG.38 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: N.193, K.195, N.205 Ligands: NAG.37 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: E.239, N.240, T.242 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: E.233, N.253 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.265, I.286, G.399 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain B: T.259, T.261, H.293, N.295, T.373 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.317 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: N.323, Q.324, R.427 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.400, T.402 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: N.226, E.257, N.406 Ligands: NAG-NAG-BMA-MAN.12 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: W.3, N.460 Chain H: N.97 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: E.55, N.56 Chain G: S.18 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain C: N.198, T.200, S.238 Ligands: NAG-NAG.18 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.240, T.242, D.243 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.265, I.286 Ligands: NAG.55 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.317 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.323, R.427 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: N.347, D.350, L.351 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain C: P.263, R.290, N.400 Ligands: NAG.51 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain C: L.229, S.255, K.404, N.406 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.20 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: W.3, N.460 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain F: N.101, S.103 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain F: R.123, N.127 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain G: N.101, S.103 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain G: N.127 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain H: N.101, S.103 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain H: R.123, E.124, N.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, J. et al., Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition. Cell Rep (2020)

Release Date

2020-04-08

Peptides

Envelope glycoprotein gp120: ABC
VRC26.25 Heavy Chain: D
VRC26.25 Light Chain: E
Envelope glycoprotein gp41: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
E

C
G

D
H

E
L

F
A

G
B

H
C

Envelope glycoprotein gp120

VRC26.25 Heavy Chain

VRC26.25 Light Chain

Envelope glycoprotein gp41

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