SMTL ID : 9fnn.1

Cryo-EM structure of the c-di-GMP-saturated 'crown'less Bcs macrocomplex for cellulose secretion in E. coli

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-4-2-2-2-2-2-mer

Ligands

6 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.1: 16 residues within 4Å: Chain A: V.695, R.696, R.697, R.700, D.723, S.725, G.727, G.728, L.729, G.730, A.763, R.764, G.771, L.772, K.773 Ligands: C2E.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.696, A:R.697, A:R.700, A:D.723, A:S.725, A:R.764 Salt bridges: A:R.700, A:D.723 pi-Cation interactions: A:R.700 C2E.2: 7 residues within 4Å: Chain A: K.693, Q.694, V.695, R.696, R.700, R.764 Ligands: C2E.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.694, A:Q.694, A:V.695, A:R.696, A:R.696, A:R.696, A:R.700, A:R.700 Salt bridges: A:R.696 pi-Cation interactions: A:R.696, A:R.764 C2E.3: 14 residues within 4Å: Chain C: L.318, R.319, A.320, R.428, D.431, L.444, S.445, C.447, R.448, D.451, T.454, A.455, H.458 Ligands: C2E.4 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.319, C:A.320, C:R.428, C:S.445, C:F.446, C:R.448 Salt bridges: C:R.428, C:D.431, C:H.458 pi-Cation interactions: C:R.428, C:R.428 C2E.4: 10 residues within 4Å: Chain C: N.286, S.317, L.318, R.319, D.322, N.427, R.428, T.429, H.458 Ligands: C2E.3 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.286, C:R.319, C:R.428, C:T.429 Salt bridges: C:R.319, C:D.322 pi-Cation interactions: C:R.319 C2E.7: 14 residues within 4Å: Chain H: L.318, R.319, A.320, R.428, D.431, L.444, S.445, F.446, C.447, D.451, T.454, A.455, H.458 Ligands: C2E.8 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:R.319, H:A.320, H:R.428, H:S.445, H:F.446 Salt bridges: H:R.428, H:D.431, H:H.458 pi-Cation interactions: H:R.428, H:R.428 C2E.8: 10 residues within 4Å: Chain H: N.286, S.317, L.318, R.319, D.322, N.427, R.428, H.458, R.516 Ligands: C2E.7 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:S.317, H:R.319, H:R.428 Salt bridges: H:R.319, H:D.322, H:R.516 pi-Cation interactions: H:R.319, H:H.458

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 22 residues within 4Å: Chain E: G.11, G.12, V.13, G.14, T.15, T.16, T.17, D.41, L.43, N.171, N.172, H.200, R.201, D.202, M.205, A.206 Chain J: R.10, D.150, A.151, N.152, R.156 Ligands: MG.6 20 PLIP interactions: 14 interactions with chain E, 6 interactions with chain J Hydrogen bonds: E:G.12, E:V.13, E:G.14, E:T.15, E:T.15, E:T.15, E:T.16, E:T.17, E:T.17, E:D.41, E:N.171, E:H.200, E:R.201, E:D.202, J:R.10, J:D.150, J:A.151, J:N.152, J:N.152 Salt bridges: J:R.156 ATP.9: 21 residues within 4Å: Chain E: R.10, D.150, A.151, N.152, R.156 Chain J: G.11, G.12, V.13, G.14, T.15, T.16, T.17, D.41, N.171, N.172, H.200, R.201, D.202, M.205, A.206 Ligands: MG.10 18 PLIP interactions: 12 interactions with chain J, 6 interactions with chain E Hydrogen bonds: J:G.12, J:V.13, J:G.14, J:T.15, J:T.15, J:T.16, J:T.16, J:T.17, J:N.171, J:N.172, J:H.200, J:D.202, E:D.150, E:D.150, E:A.151, E:N.152, E:N.152 Salt bridges: E:R.156

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain E: T.16, D.124 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.16 MG.10: 3 residues within 4Å: Chain J: T.16, D.124 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anso, I. et al., Structural basis for synthase activation and cellulose modification in the E. coli Type II Bcs secretion system. Nat Commun (2024)

Release Date

2024-10-16

Peptides

Cellulose synthase catalytic subunit [UDP-forming]: A
Cyclic di-GMP-binding protein: BKLM
Cyclic di-GMP binding protein BcsE: CH
Cellulose biosynthesis protein BcsF: DG
Cell division protein: EJ
Protein YhjR: FI
Cellulose biosynthesis protein BcsG: NO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

K
X

L
Y

M
Z

C
E

H
U

D
F

G
S

E
Q

J
W

F
R

I
V

N
G

O
D

Membrane

We predict this structure to be a membrane protein.
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Cellulose synthase catalytic subunit [UDP-forming]

Cyclic di-GMP-binding protein

Cyclic di-GMP binding protein BcsE

Cellulose biosynthesis protein BcsF

Cell division protein

Protein YhjR

Cellulose biosynthesis protein BcsG

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