SMTL ID : 4tvp.1

Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising Atomic-Level Definition of Pre-Fusion gp120 and gp41, in Complex with Human Antibodies PGT122 and 35O22

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 18 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Chain E: N.30, F.31, H.33, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain F: H.95, N.96 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.115, E:T.115, F:H.95, E:D.111, E:G.112, E:H.33, E:S.52, E:S.52, E:T.115 NAG-NAG-BMA-MAN-MAN-MAN-MAN.33: 18 residues within 4Å: Chain G: E.57, N.58 Chain H: G.16, S.17 Chain K: N.30, F.31, H.33, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain L: H.95, N.96 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:T.115, K:T.115, L:H.95, K:D.111, K:G.112, K:H.33, K:S.52, K:S.52, K:T.115 NAG-NAG-BMA-MAN-MAN-MAN-MAN.65: 18 residues within 4Å: Chain M: E.57, N.58 Chain N: G.16, S.17 Chain Q: N.30, F.31, H.33, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain R: H.95, N.96 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:T.115, Q:T.115, R:H.95, Q:D.111, Q:G.112, Q:H.33, Q:S.52, Q:S.52, Q:T.115

3 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.2: 13 residues within 4Å: Chain A: N.107, I.108, T.109 Chain C: W.88, D.89, R.92, T.94 Chain D: Y.33, D.56, N.58, R.102, F.114, T.115 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.33, D:Y.33, D:R.102, D:R.102, D:N.58, D:T.115 NAG-NAG-BMA-MAN.34: 13 residues within 4Å: Chain G: N.107, I.108, T.109 Chain I: W.88, D.89, R.92, T.94 Chain J: Y.33, D.56, N.58, R.102, F.114, T.115 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Y.33, J:Y.33, J:R.102, J:R.102, J:N.58, J:T.115 NAG-NAG-BMA-MAN.66: 13 residues within 4Å: Chain M: N.107, I.108, T.109 Chain O: W.88, D.89, R.92, T.94 Chain P: Y.33, D.56, N.58, R.102, F.114, T.115 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:Y.33, P:Y.33, P:R.102, P:R.102, P:N.58, P:T.115

24 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: 6 residues within 4Å: Chain A: N.204, T.206, S.244, I.247 Chain E: P.77, V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: N.332, S.333, S.357 Ligands: NAG-NAG.6, NAG-NAG.6, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.5, NAG-NAG.5, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.5, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: V.144, R.162, N.167 Chain M: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain A: N.265, N.301, S.303, S.381, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 6 residues within 4Å: Chain G: N.204, T.206, S.244, I.247 Chain K: P.77, V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 6 residues within 4Å: Chain G: N.332, S.333, S.357 Ligands: NAG-NAG.38, NAG-NAG.38, NAG-NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG.37, NAG-NAG.37, NAG-NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG.37, NAG-NAG.38 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 6 residues within 4Å: Chain G: T.98, Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 4 residues within 4Å: Chain A: R.278 Chain G: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 6 residues within 4Å: Chain G: N.265, N.301, S.303, S.381, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.46 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.67: 6 residues within 4Å: Chain M: N.204, T.206, S.244, I.247 Chain Q: P.77, V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.69: 6 residues within 4Å: Chain M: N.332, S.333, S.357 Ligands: NAG-NAG.70, NAG-NAG.70, NAG-NAG.71 No protein-ligand interaction detected (PLIP) NAG-NAG.70: 5 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG.69, NAG-NAG.69, NAG-NAG.71 No protein-ligand interaction detected (PLIP) NAG-NAG.71: 3 residues within 4Å: Chain M: N.361 Ligands: NAG-NAG.69, NAG-NAG.70 No protein-ligand interaction detected (PLIP) NAG-NAG.74: 6 residues within 4Å: Chain M: T.98, Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.75: 4 residues within 4Å: Chain G: R.278 Chain M: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.76: 6 residues within 4Å: Chain M: N.265, N.301, S.303, S.381, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.78 No protein-ligand interaction detected (PLIP) NAG-NAG.77: 2 residues within 4Å: Chain M: N.271, I.292 No protein-ligand interaction detected (PLIP)

3 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.4: 13 residues within 4Å: Chain A: K.35, S.179, E.181, P.182, L.231, N.232, N.346, C.347, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG-BMA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348 Water bridges: A:V.414 NAG-NAG-BMA-MAN-MAN-MAN.36: 13 residues within 4Å: Chain G: K.35, S.179, E.181, P.182, L.231, N.232, N.346, C.347, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG-BMA.40 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.348 Water bridges: G:V.414 NAG-NAG-BMA-MAN-MAN-MAN.68: 13 residues within 4Å: Chain M: K.35, S.179, E.181, P.182, L.231, N.232, N.346, C.347, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG-BMA.72 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:G.348 Water bridges: M:V.414

3 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: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.36 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.72: 4 residues within 4Å: Chain M: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.68 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.9: 5 residues within 4Å: Chain A: V.104, T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.41: 5 residues within 4Å: Chain G: V.104, T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.73: 5 residues within 4Å: Chain M: V.104, T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN.14: 20 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, D.380, T.383 Chain C: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain D: R.103, I.104, G.106, V.107, V.108 Ligands: NAG-NAG.12, SO4.23 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.296, A:R.296, D:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.46: 20 residues within 4Å: Chain G: T.267, R.296, H.299, N.301, D.380, T.383 Chain I: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain J: R.103, I.104, G.106, V.107, V.108 Ligands: NAG-NAG.44, SO4.55 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain G Hydrogen bonds: J:V.107, G:R.296, G:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.78: 20 residues within 4Å: Chain M: T.267, R.296, H.299, N.301, D.380, T.383 Chain O: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain P: R.103, I.104, G.106, V.107, V.108 Ligands: NAG-NAG.76, SO4.87 3 PLIP interactions: 1 interactions with chain P, 2 interactions with chain M Hydrogen bonds: P:V.107, M:R.296, M:R.296

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

NAG.15: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: K.320, N.324 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: T.102, N.103, D.110, K.159 Ligands: SO4.21 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: E.2 Chain B: N.107 Chain F: N.54, E.55, R.56 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: S.7, T.21, N.23 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: N.308, W.364 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain G: K.320, N.324 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain G: T.102, N.103, D.110, K.159 Ligands: SO4.53 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain G: E.2 Chain H: N.107 Chain L: N.54, E.55, R.56 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain H: E.123, N.126 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain J: S.7, T.21, N.23 Ligand excluded by PLIP NAG.79: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.80: 2 residues within 4Å: Chain M: N.308, W.364 Ligand excluded by PLIP NAG.81: 2 residues within 4Å: Chain M: K.320, N.324 Ligand excluded by PLIP NAG.82: 5 residues within 4Å: Chain M: T.102, N.103, D.110, K.159 Ligands: SO4.85 Ligand excluded by PLIP NAG.90: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP NAG.91: 5 residues within 4Å: Chain M: E.2 Chain N: N.107 Chain R: N.54, E.55, R.56 Ligand excluded by PLIP NAG.92: 2 residues within 4Å: Chain N: E.123, N.126 Ligand excluded by PLIP NAG.96: 3 residues within 4Å: Chain P: S.7, T.21, N.23 Ligand excluded by PLIP

30 x SO4: SULFATE ION(Non-functional Binders)

SO4.19: 6 residues within 4Å: Chain A: T.248, N.250, R.424, G.426, S.428, N.430 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: R.329, A.331, R.437 Ligand excluded by PLIP SO4.21: 7 residues within 4Å: Chain A: N.103, R.113, K.117, R.140, K.159, Y.161 Ligands: NAG.18 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: K.197, K.199, K.453 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain A: T.267, R.296 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain A: R.128 Chain G: R.128 Chain M: R.128 Ligands: SO4.56, SO4.88 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain A: H.75, W.395, Q.396, G.441, D.442, M.443, R.444 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain A: K.458, E.460 Chain B: R.74, R.77 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain N: R.31 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain C: D.152, S.153, K.190 Ligand excluded by PLIP SO4.51: 6 residues within 4Å: Chain G: T.248, N.250, R.424, G.426, S.428, N.430 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain G: R.329, A.331, R.437 Ligand excluded by PLIP SO4.53: 7 residues within 4Å: Chain G: N.103, R.113, K.117, R.140, K.159, Y.161 Ligands: NAG.50 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain G: K.197, K.199, K.453 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain G: T.267, R.296 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.46, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.46 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain A: R.128 Chain G: R.128 Chain M: R.128 Ligands: SO4.24, SO4.88 Ligand excluded by PLIP SO4.57: 7 residues within 4Å: Chain G: H.75, W.395, Q.396, G.441, D.442, M.443, R.444 Ligand excluded by PLIP SO4.61: 4 residues within 4Å: Chain G: K.458, E.460 Chain H: R.74, R.77 Ligand excluded by PLIP SO4.62: 1 residues within 4Å: Chain B: R.31 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain I: D.152, S.153, K.190 Ligand excluded by PLIP SO4.83: 6 residues within 4Å: Chain M: T.248, N.250, R.424, G.426, S.428, N.430 Ligand excluded by PLIP SO4.84: 3 residues within 4Å: Chain M: R.329, A.331, R.437 Ligand excluded by PLIP SO4.85: 7 residues within 4Å: Chain M: N.103, R.113, K.117, R.140, K.159, Y.161 Ligands: NAG.82 Ligand excluded by PLIP SO4.86: 3 residues within 4Å: Chain M: K.197, K.199, K.453 Ligand excluded by PLIP SO4.87: 4 residues within 4Å: Chain M: T.267, R.296 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.78, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.78 Ligand excluded by PLIP SO4.88: 5 residues within 4Å: Chain A: R.128 Chain G: R.128 Chain M: R.128 Ligands: SO4.24, SO4.56 Ligand excluded by PLIP SO4.89: 7 residues within 4Å: Chain M: H.75, W.395, Q.396, G.441, D.442, M.443, R.444 Ligand excluded by PLIP SO4.93: 4 residues within 4Å: Chain M: K.458, E.460 Chain N: R.74, R.77 Ligand excluded by PLIP SO4.94: 1 residues within 4Å: Chain H: R.31 Ligand excluded by PLIP SO4.95: 3 residues within 4Å: Chain O: D.152, S.153, K.190 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pancera, M. et al., Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature (2014)

Release Date

2014-10-08

Peptides

Envelope glycoprotein gp160: AGM
Envelope glycoprotein gp160: BHN
PGT122 Light chain: CIO
PGT122 Heavy chain: DJP
35O22 Heavy chain: EKQ
35O22 Light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

G
G

M
G

B
B

H
B

N
B

C
L

I
L

O
L

D
H

J
H

P
H

E
D

K
D

Q
D

F
E

L
E

R
E

Envelope glycoprotein gp160

Envelope glycoprotein gp160

PGT122 Light chain

PGT122 Heavy chain

35O22 Heavy chain

35O22 Light chain

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