SMTL ID : 6b0n.1

Crystal structure of the cleavage-independent prefusion HIV Env glycoprotein trimer of the clade A BG505 isolate (NFL construct) in complex with Fabs PGT122 and PGV19 at 3.39 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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.1: 10 residues within 4Å: Chain C: V.104, T.105, N.118, S.120, Y.135 Chain E: G.18, E.19, E.20, T.67 Ligands: NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.29: 10 residues within 4Å: Chain H: V.104, T.105, N.118, S.120, Y.135 Chain J: G.18, E.19, E.20, T.67 Ligands: NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.57: 10 residues within 4Å: Chain M: V.104, T.105, N.118, S.120, Y.135 Chain O: G.18, E.19, E.20, T.67 Ligands: NAG.78 No protein-ligand interaction detected (PLIP)

6 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.2: 6 residues within 4Å: Chain C: Q.100, S.120, N.122, K.131, K.133 Ligands: NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 6 residues within 4Å: Chain C: V.144, R.162, N.167, T.168 Chain M: R.278 Ligands: MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 6 residues within 4Å: Chain H: Q.100, S.120, N.122, K.131, K.133 Ligands: NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 6 residues within 4Å: Chain C: R.278 Chain H: V.144, R.162, N.167, T.168 Ligands: MAN.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.58: 6 residues within 4Å: Chain M: Q.100, S.120, N.122, K.131, K.133 Ligands: NAG.78 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.59: 6 residues within 4Å: Chain H: R.278 Chain M: V.144, R.162, N.167, T.168 Ligands: MAN.84 No protein-ligand interaction detected (PLIP)

3 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-(1-6)-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.4: 14 residues within 4Å: Chain C: P.176, P.182, V.224, L.231, N.232, R.274, N.346, G.348, V.414, S.415 Chain F: E.1, S.25 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.14, MAN.17 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:E.1, F:E.1, C:G.348 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32: 14 residues within 4Å: Chain H: P.176, P.182, V.224, L.231, N.232, R.274, N.346, G.348, V.414, S.415 Chain K: E.1, S.25 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.42, MAN.45 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain H Hydrogen bonds: K:E.1, K:E.1, H:G.348 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.60: 14 residues within 4Å: Chain A: E.1, S.25 Chain M: P.176, P.182, V.224, L.231, N.232, R.274, N.346, G.348, V.414, S.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.70, MAN.73 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain M Hydrogen bonds: A:E.1, A:E.1, M:G.348

6 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: 7 residues within 4Å: Chain A: E.104 Chain B: S.32, S.33, S.51, N.53, Y.92 Chain C: N.246 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.53 Hydrophobic interactions: A:E.104 NAG-NAG-BMA-MAN-MAN.10: 5 residues within 4Å: Chain C: N.332, S.357 Ligands: NAG-NAG.11, NAG-NAG.11, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.33: 7 residues within 4Å: Chain F: E.104 Chain G: S.32, S.33, S.51, N.53, Y.92 Chain H: N.246 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:N.53 Hydrophobic interactions: F:E.104 NAG-NAG-BMA-MAN-MAN.38: 5 residues within 4Å: Chain H: N.332, S.357 Ligands: NAG-NAG.39, NAG-NAG.39, NAG-NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.61: 7 residues within 4Å: Chain K: E.104 Chain L: S.32, S.33, S.51, N.53, Y.92 Chain M: N.246 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:N.53 Hydrophobic interactions: K:E.104 NAG-NAG-BMA-MAN-MAN.66: 5 residues within 4Å: Chain M: N.332, S.357 Ligands: NAG-NAG.67, NAG-NAG.67, NAG-NAG.69 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.6: 5 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN.10, BMA-MAN-MAN-MAN.12, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.10, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain H: Q.263, N.265, N.301, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 7 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA-MAN-MAN.38, NAG-NAG-BMA-MAN-MAN.38, BMA-MAN-MAN-MAN.40, NAG-NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 4 residues within 4Å: Chain H: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.38, NAG-NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG.62: 5 residues within 4Å: Chain M: Q.263, N.265, N.301, V.302, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.67: 7 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.66, NAG-NAG-BMA-MAN-MAN.66, NAG-NAG-BMA-MAN-MAN.66, BMA-MAN-MAN-MAN.68, NAG-NAG.69 No protein-ligand interaction detected (PLIP) NAG-NAG.69: 4 residues within 4Å: Chain M: S.357, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.66, NAG-NAG.67 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.7: 1 residues within 4Å: Chain C: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.35: 1 residues within 4Å: Chain H: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.63: 1 residues within 4Å: Chain M: N.271 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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.8: 12 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, S.381, T.383 Chain D: R.102, I.104, G.106, V.107 Ligands: MAN-MAN-MAN.9, MAN-MAN-MAN.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.102, D:R.102, D:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.36: 12 residues within 4Å: Chain H: N.265, T.267, H.299, N.301, S.381, T.383 Chain I: R.102, I.104, G.106, V.107 Ligands: MAN-MAN-MAN.37, MAN-MAN-MAN.37 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.102, I:R.102, I:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.64: 12 residues within 4Å: Chain M: N.265, T.267, H.299, N.301, S.381, T.383 Chain N: R.102, I.104, G.106, V.107 Ligands: MAN-MAN-MAN.65, MAN-MAN-MAN.65 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:R.102, N:R.102, N:V.107

3 x MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose

MAN-MAN-MAN.9: 9 residues within 4Å: Chain D: R.103, I.104, Y.105 Chain E: S.24, N.44, P.60, G.61, S.62 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) MAN-MAN-MAN.37: 9 residues within 4Å: Chain I: R.103, I.104, Y.105 Chain J: S.24, N.44, P.60, G.61, S.62 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.36 No protein-ligand interaction detected (PLIP) MAN-MAN-MAN.65: 9 residues within 4Å: Chain N: R.103, I.104, Y.105 Chain O: S.24, N.44, P.60, G.61, S.62 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.64 No protein-ligand interaction detected (PLIP)

3 x BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose

BMA-MAN-MAN-MAN.12: 2 residues within 4Å: Chain C: D.110 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.110 BMA-MAN-MAN-MAN.40: 2 residues within 4Å: Chain H: D.110 Ligands: NAG-NAG.39 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.110 BMA-MAN-MAN-MAN.68: 2 residues within 4Å: Chain M: D.110 Ligands: NAG-NAG.67 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:D.110

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: 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.14: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.42: 4 residues within 4Å: Chain H: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.70: 4 residues within 4Å: Chain M: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.60 No protein-ligand interaction detected (PLIP)

36 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.15: 9 residues within 4Å: Chain C: N.107, I.108, T.109 Chain D: F.114, T.115 Chain E: W.88, D.89, R.92, T.94 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Ligands: NAG.26 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: N.585, S.587 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain C: N.590, R.591, N.592, E.595 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: E.608, N.611 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain C: Q.100, T.102, N.158 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: E.57, N.58 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.103, R.113, K.117, Y.161 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.599 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.204, H.321 Ligands: NAG.16 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.43: 9 residues within 4Å: Chain H: N.107, I.108, T.109 Chain I: F.114, T.115 Chain J: W.88, D.89, R.92, T.94 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Ligands: NAG.54 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain H: N.585, S.587 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain H: N.590, R.591, N.592, E.595 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain H: E.608, N.611 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain H: N.308 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain H: Q.100, T.102, N.158 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.29, NAG-NAG-BMA.30 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain H: E.57, N.58 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain H: N.103, R.113, K.117, Y.161 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain H: N.599 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain H: N.204, H.321 Ligands: NAG.44 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain H: N.324 Ligand excluded by PLIP NAG.71: 9 residues within 4Å: Chain M: N.107, I.108, T.109 Chain N: F.114, T.115 Chain O: W.88, D.89, R.92, T.94 Ligand excluded by PLIP NAG.72: 1 residues within 4Å: Ligands: NAG.82 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain M: N.585, S.587 Ligand excluded by PLIP NAG.75: 4 residues within 4Å: Chain M: N.590, R.591, N.592, E.595 Ligand excluded by PLIP NAG.76: 2 residues within 4Å: Chain M: E.608, N.611 Ligand excluded by PLIP NAG.77: 1 residues within 4Å: Chain M: N.308 Ligand excluded by PLIP NAG.78: 5 residues within 4Å: Chain M: Q.100, T.102, N.158 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.57, NAG-NAG-BMA.58 Ligand excluded by PLIP NAG.79: 2 residues within 4Å: Chain M: E.57, N.58 Ligand excluded by PLIP NAG.80: 4 residues within 4Å: Chain M: N.103, R.113, K.117, Y.161 Ligand excluded by PLIP NAG.81: 1 residues within 4Å: Chain M: N.599 Ligand excluded by PLIP NAG.82: 3 residues within 4Å: Chain M: N.204, H.321 Ligands: NAG.72 Ligand excluded by PLIP NAG.83: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP

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

MAN.17: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) MAN.28: 1 residues within 4Å: Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) MAN.45: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32 No protein-ligand interaction detected (PLIP) MAN.56: 1 residues within 4Å: Ligands: NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP) MAN.73: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.60, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.60 No protein-ligand interaction detected (PLIP) MAN.84: 1 residues within 4Å: Ligands: NAG-NAG-BMA.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sarkar, A. et al., Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer. Nat Commun (2018)

Release Date

2018-05-30

Peptides

PGV19 Fab heavy chain: AFK
PGV19 light chain: BGL
Envelope glycoprotein gp140: CHM
PGT122 Fab heavy chain: DIN
PGT122 light chain: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

F
D

K
D

B
E

G
E

L
E

C
G

H
G

M
G

D
H

I
H

N
H

E
L

J
L

O
L

PGV19 Fab heavy chain

PGV19 light chain

Envelope glycoprotein gp140

PGT122 Fab heavy chain

PGT122 light chain

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