SMTL ID : 9auh.1

Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 10 residues within 4Å: Chain A: E.171, V.214, L.221, N.222, N.335, C.336, G.337, C.401, R.402, S.403 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.337 NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain B: T.169, L.221, N.222, C.336, G.337, R.402, S.403 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.337 NAG-NAG-BMA-MAN-MAN.9: 9 residues within 4Å: Chain C: T.169, V.214, L.221, N.222, N.335, G.337, R.402, S.403 Ligands: NAG.40 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.337

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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.2: 18 residues within 4Å: Chain A: T.257, H.289, N.291, T.369, T.371 Chain G: T.28, Y.32, R.98, G.99, W.101, S.103, Y.105, Y.106, N.113, D.115 Chain J: Y.51, E.52, S.58 No protein-ligand interaction detected (PLIP)

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.3: 10 residues within 4Å: Chain A: N.260, N.261, N.262, I.282 Chain J: Q.1, Y.32, Y.93, A.94, G.95, S.96 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Q.1, J:A.94 NAG-NAG-BMA.7: 10 residues within 4Å: Chain B: N.260, N.261, N.262, I.282 Chain L: Q.1, Y.32, Y.93, A.94, S.96, S.97 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Q.1, L:A.94 NAG-NAG-BMA.11: 10 residues within 4Å: Chain C: N.260, N.261, N.262, T.263, I.282 Chain K: Q.1, Y.32, Y.93, A.94, S.96 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Q.1, K:A.94

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

NAG-NAG.4: 5 residues within 4Å: Chain A: G.105, N.114, S.116, Y.131, L.133 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: A.104, N.114, Y.131, L.133, D.280 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.114, Y.131, D.280 No protein-ligand interaction detected (PLIP)

2 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.6: 17 residues within 4Å: Chain B: T.257, H.289, N.291, T.369, T.371 Chain H: T.28, Y.32, R.98, W.101, S.103, Y.105, Y.106, Y.111, N.113, D.115 Chain L: Y.51, E.52 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:T.28 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.10: 16 residues within 4Å: Chain C: T.257, H.289, N.291, T.369, T.371 Chain I: Y.32, G.99, W.101, S.103, Y.105, Y.106, N.113, D.115 Chain K: Y.51, E.52, K.55 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: T.330, N.344, S.346 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: Q.321, N.350 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: I.100, N.118, K.129 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: K.318, N.320, R.425 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.236, T.238, N.239 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.58 Chain D: T.18 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.189, N.201 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.222, E.253, N.404 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.398, T.400 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: V.140, N.157 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: T.330, N.344, S.346 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.350 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: I.100, N.118, K.129 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: K.318, Y.319, N.320, R.425 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.236, T.238, N.239 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: G.57, N.58 Chain E: S.17 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.189, N.201 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.222, N.404 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.398, T.400 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.157 Chain C: R.268 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: T.330, N.344, S.346 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.350 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.118, K.129 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: K.318, Y.319, N.320, R.425 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.236, T.238 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: G.57, N.58 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: V.55, N.189, N.201 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.222, P.251, N.404 Ligands: NAG-NAG-BMA-MAN-MAN.9 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.398, I.399, T.400 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: V.140, N.157, T.158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swanson, O.M. et al., An engineered immunogen activates diverse HIV broadly neutralizing antibody precursors and promotes acquisition of improbable mutations. Sci Transl Med (2025)

Release Date

2025-02-05

Peptides

HIV-1 BG505 DS-SOSIP glycoprotein gp120: ABC
HIV-1 BG505 DS-SOSIP glycoprotein gp41: DEF
UCA3 heavy chain: GHI
UCA3 light chain: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

HIV-1 BG505 DS-SOSIP glycoprotein gp120

HIV-1 BG505 DS-SOSIP glycoprotein gp41

UCA3 heavy chain

UCA3 light chain

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