SMTL ID : 6vy2.1

Cryo-EM structure of M1214_N1 Fab in complex with CH505 TF chimeric SOSIP.664 Env trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-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: 4 residues within 4Å: Chain A: K.81, N.82 Chain B: G.23, S.24 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.124, Q.175 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: S.143, F.144, N.145, R.154, K.156 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.318, S.320, K.321, E.324 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain A: Q.345, K.443, N.444 Chain G: R.2 Ligands: NAG.52 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.2, G:R.2 NAG-NAG.17: 4 residues within 4Å: Chain C: K.81, N.82 Chain D: G.23, S.24 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.124, Q.175 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain C: S.143, F.144, N.145, R.154, K.156 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: N.318, S.320, K.321, E.324 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 5 residues within 4Å: Chain C: Q.345, K.443, N.444 Chain H: R.2 Ligands: NAG.60 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.2, H:R.2 NAG-NAG.33: 4 residues within 4Å: Chain E: K.81, N.82 Chain F: G.23, S.24 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain E: N.124, Q.175 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain E: F.144, N.145, R.154, K.156 Ligands: NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 4 residues within 4Å: Chain E: N.318, S.320, K.321, E.324 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 5 residues within 4Å: Chain E: Q.345, K.443, N.444 Chain I: R.2 Ligands: NAG.68 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.2

21 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.3: 1 residues within 4Å: Chain A: N.127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: N.215, T.217, F.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 3 residues within 4Å: Chain A: N.261, T.263, N.264 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 6 residues within 4Å: Chain A: G.253, E.254, N.274, E.275, R.328, K.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.328, A:R.328, A:K.331 NAG-NAG-BMA.12: 6 residues within 4Å: Chain A: E.319, N.323, R.376, S.388, E.390 Ligands: NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain A: N.375 Ligands: NAG-NAG-BMA.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 2 residues within 4Å: Chain A: N.431 Ligands: NAG-NAG-BMA-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 1 residues within 4Å: Chain C: N.127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 3 residues within 4Å: Chain C: N.215, T.217, F.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 3 residues within 4Å: Chain C: N.261, T.263, N.264 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 6 residues within 4Å: Chain C: G.253, E.254, N.274, E.275, R.328, K.331 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.328, C:R.328, C:K.331 NAG-NAG-BMA.28: 6 residues within 4Å: Chain C: E.319, N.323, R.376, S.388, E.390 Ligands: NAG-NAG-BMA.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 4 residues within 4Å: Chain C: N.375 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA-MAN-MAN-MAN-MAN.29, NAG-NAG-BMA-MAN-MAN-MAN-MAN.29 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 2 residues within 4Å: Chain C: N.431 Ligands: NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 1 residues within 4Å: Chain E: N.127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 4 residues within 4Å: Chain E: N.215, T.217, F.218, T.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 3 residues within 4Å: Chain E: N.261, T.263, N.264 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 6 residues within 4Å: Chain E: G.253, E.254, N.274, E.275, R.328, K.331 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:E.254 Hydrogen bonds: E:R.328, E:R.328, E:K.331 NAG-NAG-BMA.44: 6 residues within 4Å: Chain E: E.319, N.323, R.376, S.388, E.390 Ligands: NAG-NAG-BMA.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 4 residues within 4Å: Chain E: N.375 Ligands: NAG-NAG-BMA.44, NAG-NAG-BMA-MAN-MAN-MAN-MAN.45, NAG-NAG-BMA-MAN-MAN-MAN-MAN.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.47: 2 residues within 4Å: Chain E: N.431 Ligands: NAG-NAG-BMA-MAN-MAN.40 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.5: 13 residues within 4Å: Chain A: D.170, R.177, N.182, T.183 Chain C: W.299 Chain G: D.60 Chain J: G.29, A.30, A.31, G.95, F.97, T.98, F.99 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain G Hydrophobic interactions: J:A.31 Hydrogen bonds: J:A.30, J:A.31, G:D.60, J:S.2, J:S.2 NAG-NAG-BMA-MAN-MAN.21: 10 residues within 4Å: Chain C: D.170, R.177, N.182, T.183 Chain H: D.60 Chain K: G.29, A.30, A.31, F.97, T.98 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain H Hydrogen bonds: K:A.30, K:A.31, H:D.60 NAG-NAG-BMA-MAN-MAN.37: 11 residues within 4Å: Chain A: W.299 Chain E: D.170, R.177, N.182, T.183 Chain I: D.60 Chain L: G.29, A.30, A.31, F.97, T.98 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain I Hydrogen bonds: L:A.30, L:A.31, I:D.60

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.7: 4 residues within 4Å: Chain A: E.77, N.214, N.225, N.226 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 4 residues within 4Å: Chain C: E.77, N.214, N.225, N.226 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.39: 4 residues within 4Å: Chain E: E.77, N.214, N.225, N.226 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.77, E:E.77

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.8: 10 residues within 4Å: Chain A: S.194, D.196, P.197, N.247, C.361, C.428, I.429, S.430, N.431 Ligands: NAG-NAG-BMA.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.196 Hydrogen bonds: A:S.194, A:S.194, A:D.196 NAG-NAG-BMA-MAN-MAN.24: 9 residues within 4Å: Chain C: S.194, D.196, P.197, N.247, C.361, I.429, S.430, N.431 Ligands: NAG-NAG-BMA.31 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.196 Hydrogen bonds: C:S.194, C:S.194, C:D.196 NAG-NAG-BMA-MAN-MAN.40: 9 residues within 4Å: Chain E: S.194, D.196, P.197, N.247, C.361, I.429, S.430, N.431 Ligands: NAG-NAG-BMA.47 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:D.196 Hydrogen bonds: E:S.194, E:S.194, E:D.196

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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.13: 8 residues within 4Å: Chain A: L.352, N.369, S.371 Chain G: D.113 Chain J: R.47, W.57 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.29: 8 residues within 4Å: Chain C: L.352, N.369, S.371 Chain H: D.113 Chain K: R.47, W.57 Ligands: NAG-NAG-BMA.30, NAG-NAG-BMA.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.45: 9 residues within 4Å: Chain E: L.352, N.369, S.371, R.402 Chain I: D.113 Chain L: R.47, W.57 Ligands: NAG-NAG-BMA.46, NAG-NAG-BMA.46 No protein-ligand interaction detected (PLIP)

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

NAG.49: 3 residues within 4Å: Chain A: T.129, K.140, N.141 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain A: N.172, S.173, S.174 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain A: P.284, N.286, I.307, G.308 Ligand excluded by PLIP NAG.52: 6 residues within 4Å: Chain A: K.340, N.341, M.379, N.445, T.446 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain A: N.425, I.426, T.427 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain B: N.107 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain B: N.114, E.117 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain B: N.133, Y.134 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: T.129, K.140, N.141 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain C: N.172, S.173, S.174 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain C: P.284, N.286, I.307, G.308 Ligand excluded by PLIP NAG.60: 6 residues within 4Å: Chain C: K.340, N.341, M.379, N.445, T.446 Ligands: NAG-NAG.32 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain C: N.425, I.426, T.427 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain D: N.107 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain D: N.114, E.117 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain D: N.133, Y.134 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain E: K.140, N.141, N.158 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain E: N.172, S.173, S.174 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain E: P.284, N.286, I.307, G.308 Ligand excluded by PLIP NAG.68: 6 residues within 4Å: Chain E: K.340, N.341, M.379, N.445, T.446 Ligands: NAG-NAG.48 Ligand excluded by PLIP NAG.69: 3 residues within 4Å: Chain E: N.425, I.426, T.427 Ligand excluded by PLIP NAG.70: 1 residues within 4Å: Chain F: N.107 Ligand excluded by PLIP NAG.71: 2 residues within 4Å: Chain F: N.114, E.117 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain F: N.133, Y.134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, M. et al., VSV-Displayed HIV-1 Envelope Identifies Broadly Neutralizing Antibodies Class-Switched to IgG and IgA. Cell Host Microbe (2020)

Release Date

2020-05-06

Peptides

Glycoprotein 120: ACE
Glycoprotein 41: BDF
M1214 N1 Fab heavy chain: GHI
M1214 N1 Fab light chain: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
I

I
J

J
L

K
M

L
N

Glycoprotein 120

Glycoprotein 41

M1214 N1 Fab heavy chain

M1214 N1 Fab light chain

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