SMTL ID : 9d90.1

Cryo-EM structure of partially open HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-17b Fab and 3-VRC34.01 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.91 Å

Oligo State

hetero-3-3-3-3-3-3-3-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: 6 residues within 4Å: Chain A: N.56 Chain D: T.18, D.113 Chain G: Y.102 Chain H: N.31, Y.50 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D Hydrogen bonds: H:N.31 Hydrophobic interactions: D:T.18 NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain B: N.56 Chain E: S.17, D.113 Chain J: R.30, N.31, Y.49, Y.50 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.31, J:Y.49, J:Y.49 NAG-NAG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain C: N.56 Chain F: A.21 Chain K: Y.102 Chain L: R.30, N.31, Y.50 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain F Hydrogen bonds: L:R.30, L:R.30, L:N.31 Hydrophobic interactions: F:A.21

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

NAG.4: 2 residues within 4Å: Chain D: N.100, S.102 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.102 NAG.5: 2 residues within 4Å: Chain E: N.100, S.102 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.102 NAG.6: 2 residues within 4Å: Chain F: N.100, S.102 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.100, F:S.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thakur, B. et al., Cryo-EM structure of partially open HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-17b Fab and 3-VRC34.01 Fab. To Be Published

Release Date

2025-04-30

Peptides

Surface protein gp120: ABC
Transmembrane protein gp41: DEF
VRC34.01 heavy chain: GIK
VRC34.01 light chain: HJL
T-cell surface glycoprotein CD4: MNO
17b Fab light chain: PRT
17b Fab heavy chain: QSU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

I
I

K
K

H
H

J
J

L
L

M
M

N
N

O
O

P
P

R
R

T
T

Q
Q

S
S

U
U

Surface protein gp120

Transmembrane protein gp41

VRC34.01 heavy chain

VRC34.01 light chain

T-cell surface glycoprotein CD4

17b Fab light chain

17b Fab heavy chain

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