SMTL ID : 7peo.1

Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.37 Å

Oligo State

homo-14-mer

Ligands

14 x BMA- MRH- MRH- BMA- MRH- MRH- BMA- MRH- MRH- BMA- MRH- MRH: 4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose

BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.1: 19 residues within 4Å: Chain A: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.29 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.5: 19 residues within 4Å: Chain B: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.33 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.9: 19 residues within 4Å: Chain C: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.37 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.13: 20 residues within 4Å: Chain D: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.53, BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.53 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.17: 19 residues within 4Å: Chain E: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.49 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.21: 19 residues within 4Å: Chain F: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.45 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.25: 19 residues within 4Å: Chain G: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.41 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.29: 19 residues within 4Å: Chain H: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.1 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.33: 19 residues within 4Å: Chain I: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.5 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.37: 19 residues within 4Å: Chain J: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.9 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.41: 19 residues within 4Å: Chain K: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.25 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.45: 19 residues within 4Å: Chain L: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.21 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.49: 19 residues within 4Å: Chain M: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.17 No protein-ligand interaction detected (PLIP) BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.53: 19 residues within 4Å: Chain N: Y.64, P.72, S.73, L.80, N.86, N.88, Y.94, Y.95, F.98, N.106, F.107, N.110, G.116, A.117, N.178, T.179, P.180, A.232 Ligands: BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH-BMA-MRH-MRH.13 No protein-ligand interaction detected (PLIP)

28 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.83, A:N.86, A:D.89, A:D.92 CA.4: 3 residues within 4Å: Chain A: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.221, A:D.221, A:D.224, A:D.224, A:A.226 CA.6: 5 residues within 4Å: Chain B: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.83, B:N.86, B:D.89, B:D.92 CA.8: 3 residues within 4Å: Chain B: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.221, B:D.221, B:D.224, B:D.224, B:A.226 CA.10: 5 residues within 4Å: Chain C: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:S.83, C:N.86, C:D.89, C:D.92 CA.12: 3 residues within 4Å: Chain C: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.221, C:D.221, C:D.224, C:D.224, C:A.226 CA.14: 5 residues within 4Å: Chain D: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:S.83, D:N.86, D:D.89, D:D.92 CA.16: 3 residues within 4Å: Chain D: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.221, D:D.221, D:D.224, D:D.224, D:A.226 CA.18: 5 residues within 4Å: Chain E: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:S.83, E:N.86, E:D.89, E:D.92 CA.20: 3 residues within 4Å: Chain E: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.221, E:D.221, E:D.224, E:D.224, E:A.226 CA.22: 5 residues within 4Å: Chain F: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:S.83, F:N.86, F:D.89, F:D.92 CA.24: 3 residues within 4Å: Chain F: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.221, F:D.221, F:D.224, F:D.224, F:A.226 CA.26: 5 residues within 4Å: Chain G: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:S.83, G:N.86, G:D.89, G:D.92 CA.28: 3 residues within 4Å: Chain G: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.221, G:D.221, G:D.224, G:D.224, G:A.226 CA.30: 5 residues within 4Å: Chain H: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:S.83, H:N.86, H:D.89, H:D.92 CA.32: 3 residues within 4Å: Chain H: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.221, H:D.221, H:D.224, H:D.224, H:A.226 CA.34: 5 residues within 4Å: Chain I: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:S.83, I:N.86, I:D.89, I:D.92 CA.36: 3 residues within 4Å: Chain I: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.221, I:D.221, I:D.224, I:D.224, I:A.226 CA.38: 5 residues within 4Å: Chain J: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:S.83, J:N.86, J:D.89, J:D.92 CA.40: 3 residues within 4Å: Chain J: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.221, J:D.221, J:D.224, J:D.224, J:A.226 CA.42: 5 residues within 4Å: Chain K: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:S.83, K:N.86, K:D.89, K:D.92 CA.44: 3 residues within 4Å: Chain K: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.221, K:D.221, K:D.224, K:D.224, K:A.226 CA.46: 5 residues within 4Å: Chain L: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:S.83, L:N.86, L:D.89, L:D.92 CA.48: 3 residues within 4Å: Chain L: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:D.221, L:D.221, L:D.224, L:D.224, L:A.226 CA.50: 5 residues within 4Å: Chain M: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:S.83, M:N.86, M:D.89, M:D.92 CA.52: 3 residues within 4Å: Chain M: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:D.221, M:D.221, M:D.224, M:D.224, M:A.226 CA.54: 5 residues within 4Å: Chain N: S.83, N.86, T.87, D.89, D.92 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:S.83, N:N.86, N:D.89, N:D.92 CA.56: 3 residues within 4Å: Chain N: D.221, D.224, A.226 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:D.221, N:D.221, N:D.224, N:D.224, N:A.226

14 x HO: HOLMIUM ATOM(Non-covalent)

HO.3: 3 residues within 4Å: Chain A: L.16, D.78, D.82 Ligand excluded by PLIP HO.7: 3 residues within 4Å: Chain B: L.16, D.78, D.82 Ligand excluded by PLIP HO.11: 3 residues within 4Å: Chain C: L.16, D.78, D.82 Ligand excluded by PLIP HO.15: 3 residues within 4Å: Chain D: L.16, D.78, D.82 Ligand excluded by PLIP HO.19: 3 residues within 4Å: Chain E: L.16, D.78, D.82 Ligand excluded by PLIP HO.23: 3 residues within 4Å: Chain F: L.16, D.78, D.82 Ligand excluded by PLIP HO.27: 3 residues within 4Å: Chain G: L.16, D.78, D.82 Ligand excluded by PLIP HO.31: 3 residues within 4Å: Chain H: L.16, D.78, D.82 Ligand excluded by PLIP HO.35: 3 residues within 4Å: Chain I: L.16, D.78, D.82 Ligand excluded by PLIP HO.39: 3 residues within 4Å: Chain J: L.16, D.78, D.82 Ligand excluded by PLIP HO.43: 3 residues within 4Å: Chain K: L.16, D.78, D.82 Ligand excluded by PLIP HO.47: 3 residues within 4Å: Chain L: L.16, D.78, D.82 Ligand excluded by PLIP HO.51: 3 residues within 4Å: Chain M: L.16, D.78, D.82 Ligand excluded by PLIP HO.55: 3 residues within 4Å: Chain N: L.16, D.78, D.82 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herdman, M. et al., High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells. Structure (2022)

Release Date

2021-12-01

Peptides

S-layer protein: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

S-layer protein

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