SMTL ID : 8dft.1

Cryo-EM structure of conjugative pili from Pyrobaculum calidifontis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-20-mer

Ligands

20 x TT0: [(2~{S},7~{S},11~{S},15~{S},19~{R},22~{R},26~{S},30~{R},34~{R},38~{S},43~{S},47~{S},51~{S},55~{R},58~{R},62~{S},66~{R},70~{R})-38-(hydroxymethyl)-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methanol(Non-covalent)

TT0.1: 18 residues within 4Å: Chain A: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain L: W.6 Chain P: K.60, G.75, G.79, I.83 Chain T: I.56, K.60, L.63, F.67 Ligands: TT0.12 17 PLIP interactions: 5 interactions with chain T, 8 interactions with chain A, 2 interactions with chain P, 2 interactions with chain L Hydrophobic interactions: T:I.56, T:I.56, T:K.60, T:L.63, T:F.67, A:I.9, A:W.16, A:W.16, A:I.23, A:I.30, A:L.31, A:F.34, P:I.83, P:I.83, L:W.6, L:W.6 Hydrogen bonds: A:Y.35 TT0.2: 16 residues within 4Å: Chain B: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain F: I.56, K.60, L.63, F.67 Chain G: F.34, M.38, V.41 Ligands: TT0.7 15 PLIP interactions: 8 interactions with chain B, 5 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: B:I.9, B:W.16, B:W.16, B:I.23, B:I.30, B:L.31, B:F.34, F:I.56, F:I.56, F:K.60, F:L.63, F:F.67, G:F.34, G:V.41 Hydrogen bonds: B:Y.35 TT0.3: 20 residues within 4Å: Chain B: K.60, G.75, G.79, I.83 Chain C: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain G: I.56, K.60, L.63, F.67 Chain H: F.34, M.38, V.41 Ligands: TT0.8 17 PLIP interactions: 5 interactions with chain G, 2 interactions with chain H, 8 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: G:I.56, G:I.56, G:K.60, G:L.63, G:F.67, H:F.34, H:V.41, C:I.9, C:W.16, C:W.16, C:I.23, C:I.30, C:L.31, C:F.34, B:I.83, B:I.83 Hydrogen bonds: C:Y.35 TT0.4: 20 residues within 4Å: Chain C: K.60, G.75, G.79, I.83 Chain D: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain H: I.56, K.60, L.63, F.67 Chain I: F.34, M.38, V.41 Ligands: TT0.9 17 PLIP interactions: 5 interactions with chain H, 8 interactions with chain D, 2 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: H:I.56, H:I.56, H:K.60, H:L.63, H:F.67, D:I.9, D:W.16, D:W.16, D:I.23, D:I.30, D:L.31, D:F.34, C:I.83, C:I.83, I:F.34, I:V.41 Hydrogen bonds: D:Y.35 TT0.5: 20 residues within 4Å: Chain D: K.60, G.75, G.79, I.83 Chain E: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain I: I.56, K.60, L.63, F.67 Chain J: F.34, M.38, V.41 Ligands: TT0.10 17 PLIP interactions: 8 interactions with chain E, 2 interactions with chain J, 5 interactions with chain I, 2 interactions with chain D Hydrophobic interactions: E:I.9, E:W.16, E:W.16, E:I.23, E:I.30, E:L.31, E:F.34, J:F.34, J:V.41, I:I.56, I:I.56, I:K.60, I:L.63, I:F.67, D:I.83, D:I.83 Hydrogen bonds: E:Y.35 TT0.6: 20 residues within 4Å: Chain E: K.60, G.75, G.79, I.83 Chain F: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain J: I.56, K.60, L.63, F.67 Chain K: F.34, M.38, V.41 Ligands: TT0.11 17 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E, 2 interactions with chain K, 5 interactions with chain J Hydrophobic interactions: F:I.9, F:W.16, F:W.16, F:I.23, F:I.30, F:L.31, F:F.34, E:I.83, E:I.83, K:F.34, K:V.41, J:I.56, J:I.56, J:K.60, J:L.63, J:F.67 Hydrogen bonds: F:Y.35 TT0.7: 22 residues within 4Å: Chain B: W.6 Chain F: K.60, G.75, G.79, I.83 Chain G: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain K: I.56, K.60, L.63, F.67 Chain L: F.34, M.38, V.41 Ligands: TT0.2, TT0.12 19 PLIP interactions: 8 interactions with chain G, 2 interactions with chain L, 5 interactions with chain K, 2 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: G:I.9, G:W.16, G:W.16, G:I.23, G:I.30, G:L.31, G:F.34, L:F.34, L:V.41, K:I.56, K:I.56, K:K.60, K:L.63, K:F.67, F:I.83, F:I.83, B:W.6, B:W.6 Hydrogen bonds: G:Y.35 TT0.8: 22 residues within 4Å: Chain C: W.6 Chain G: K.60, G.75, G.79, I.83 Chain H: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain L: I.56, K.60, L.63, F.67 Chain M: F.34, M.38, V.41 Ligands: TT0.3, TT0.13 19 PLIP interactions: 8 interactions with chain H, 2 interactions with chain C, 5 interactions with chain L, 2 interactions with chain M, 2 interactions with chain G Hydrophobic interactions: H:I.9, H:W.16, H:W.16, H:I.23, H:I.30, H:L.31, H:F.34, C:W.6, C:W.6, L:I.56, L:I.56, L:K.60, L:L.63, L:F.67, M:F.34, M:V.41, G:I.83, G:I.83 Hydrogen bonds: H:Y.35 TT0.9: 22 residues within 4Å: Chain D: W.6 Chain H: K.60, G.75, G.79, I.83 Chain I: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain M: I.56, K.60, L.63, F.67 Chain N: F.34, M.38, V.41 Ligands: TT0.4, TT0.14 19 PLIP interactions: 5 interactions with chain M, 8 interactions with chain I, 2 interactions with chain N, 2 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: M:I.56, M:I.56, M:K.60, M:L.63, M:F.67, I:I.9, I:W.16, I:W.16, I:I.23, I:I.30, I:L.31, I:F.34, N:F.34, N:V.41, H:I.83, H:I.83, D:W.6, D:W.6 Hydrogen bonds: I:Y.35 TT0.10: 22 residues within 4Å: Chain E: W.6 Chain I: K.60, G.75, G.79, I.83 Chain J: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain N: I.56, K.60, L.63, F.67 Chain O: F.34, M.38, V.41 Ligands: TT0.5, TT0.15 19 PLIP interactions: 8 interactions with chain J, 5 interactions with chain N, 2 interactions with chain O, 2 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: J:I.9, J:W.16, J:W.16, J:I.23, J:I.30, J:L.31, J:F.34, N:I.56, N:I.56, N:K.60, N:L.63, N:F.67, O:F.34, O:V.41, I:I.83, I:I.83, E:W.6, E:W.6 Hydrogen bonds: J:Y.35 TT0.11: 22 residues within 4Å: Chain F: W.6 Chain J: K.60, G.75, G.79, I.83 Chain K: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain O: I.56, K.60, L.63, F.67 Chain P: F.34, M.38, V.41 Ligands: TT0.6, TT0.16 19 PLIP interactions: 2 interactions with chain P, 5 interactions with chain O, 8 interactions with chain K, 2 interactions with chain J, 2 interactions with chain F Hydrophobic interactions: P:F.34, P:V.41, O:I.56, O:I.56, O:K.60, O:L.63, O:F.67, K:I.9, K:W.16, K:W.16, K:I.23, K:I.30, K:L.31, K:F.34, J:I.83, J:I.83, F:W.6, F:W.6 Hydrogen bonds: K:Y.35 TT0.12: 22 residues within 4Å: Chain A: F.34, M.38, V.41 Chain G: W.6 Chain K: K.60, G.75, G.79, I.83 Chain L: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain P: I.56, K.60, L.63, F.67 Ligands: TT0.1, TT0.7 19 PLIP interactions: 5 interactions with chain P, 8 interactions with chain L, 2 interactions with chain G, 2 interactions with chain A, 2 interactions with chain K Hydrophobic interactions: P:I.56, P:I.56, P:K.60, P:L.63, P:F.67, L:I.9, L:W.16, L:W.16, L:I.23, L:I.30, L:L.31, L:F.34, G:W.6, G:W.6, A:F.34, A:V.41, K:I.83, K:I.83 Hydrogen bonds: L:Y.35 TT0.13: 22 residues within 4Å: Chain A: I.56, K.60, L.63, F.67 Chain H: W.6 Chain L: K.60, G.75, G.79, I.83 Chain M: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain Q: F.34, M.38, V.41 Ligands: TT0.8, TT0.17 19 PLIP interactions: 5 interactions with chain A, 8 interactions with chain M, 2 interactions with chain Q, 2 interactions with chain H, 2 interactions with chain L Hydrophobic interactions: A:I.56, A:I.56, A:K.60, A:L.63, A:F.67, M:I.9, M:W.16, M:W.16, M:I.23, M:I.30, M:L.31, M:F.34, Q:F.34, Q:V.41, H:W.6, H:W.6, L:I.83, L:I.83 Hydrogen bonds: M:Y.35 TT0.14: 22 residues within 4Å: Chain I: W.6 Chain M: K.60, G.75, G.79, I.83 Chain N: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain Q: I.56, K.60, L.63, F.67 Chain R: F.34, M.38, V.41 Ligands: TT0.9, TT0.18 19 PLIP interactions: 8 interactions with chain N, 5 interactions with chain Q, 2 interactions with chain R, 2 interactions with chain M, 2 interactions with chain I Hydrophobic interactions: N:I.9, N:W.16, N:W.16, N:I.23, N:I.30, N:L.31, N:F.34, Q:I.56, Q:I.56, Q:K.60, Q:L.63, Q:F.67, R:F.34, R:V.41, M:I.83, M:I.83, I:W.6, I:W.6 Hydrogen bonds: N:Y.35 TT0.15: 22 residues within 4Å: Chain J: W.6 Chain N: K.60, G.75, G.79, I.83 Chain O: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain R: I.56, K.60, L.63, F.67 Chain S: F.34, M.38, V.41 Ligands: TT0.10, TT0.19 19 PLIP interactions: 2 interactions with chain S, 8 interactions with chain O, 5 interactions with chain R, 2 interactions with chain J, 2 interactions with chain N Hydrophobic interactions: S:F.34, S:V.41, O:I.9, O:W.16, O:W.16, O:I.23, O:I.30, O:L.31, O:F.34, R:I.56, R:I.56, R:K.60, R:L.63, R:F.67, J:W.6, J:W.6, N:I.83, N:I.83 Hydrogen bonds: O:Y.35 TT0.16: 22 residues within 4Å: Chain K: W.6 Chain O: K.60, G.75, G.79, I.83 Chain P: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Chain S: I.56, K.60, L.63, F.67 Chain T: F.34, M.38, V.41 Ligands: TT0.11, TT0.20 19 PLIP interactions: 2 interactions with chain K, 8 interactions with chain P, 5 interactions with chain S, 2 interactions with chain T, 2 interactions with chain O Hydrophobic interactions: K:W.6, K:W.6, P:I.9, P:W.16, P:W.16, P:I.23, P:I.30, P:L.31, P:F.34, S:I.56, S:I.56, S:K.60, S:L.63, S:F.67, T:F.34, T:V.41, O:I.83, O:I.83 Hydrogen bonds: P:Y.35 TT0.17: 14 residues within 4Å: Chain A: K.60, G.75, G.79, I.83 Chain M: W.6 Chain Q: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Ligands: TT0.13 12 PLIP interactions: 8 interactions with chain Q, 2 interactions with chain A, 2 interactions with chain M Hydrophobic interactions: Q:I.9, Q:W.16, Q:W.16, Q:I.23, Q:I.30, Q:L.31, Q:F.34, A:I.83, A:I.83, M:W.6, M:W.6 Hydrogen bonds: Q:Y.35 TT0.18: 14 residues within 4Å: Chain N: W.6 Chain Q: K.60, G.75, G.79, I.83 Chain R: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Ligands: TT0.14 12 PLIP interactions: 8 interactions with chain R, 2 interactions with chain N, 2 interactions with chain Q Hydrophobic interactions: R:I.9, R:W.16, R:W.16, R:I.23, R:I.30, R:L.31, R:F.34, N:W.6, N:W.6, Q:I.83, Q:I.83 Hydrogen bonds: R:Y.35 TT0.19: 14 residues within 4Å: Chain O: W.6 Chain R: K.60, G.75, G.79, I.83 Chain S: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Ligands: TT0.15 12 PLIP interactions: 8 interactions with chain S, 2 interactions with chain O, 2 interactions with chain R Hydrophobic interactions: S:I.9, S:W.16, S:W.16, S:I.23, S:I.30, S:L.31, S:F.34, O:W.6, O:W.6, R:I.83, R:I.83 Hydrogen bonds: S:Y.35 TT0.20: 14 residues within 4Å: Chain P: W.6 Chain S: K.60, G.75, G.79, I.83 Chain T: I.9, W.16, I.23, S.27, I.30, L.31, F.34, Y.35 Ligands: TT0.16 12 PLIP interactions: 2 interactions with chain S, 8 interactions with chain T, 2 interactions with chain P Hydrophobic interactions: S:I.83, S:I.83, T:I.9, T:W.16, T:W.16, T:I.23, T:I.30, T:L.31, T:F.34, P:W.6, P:W.6 Hydrogen bonds: T:Y.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beltran, L.C. et al., Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery. Nat Commun (2023)

Release Date

2023-03-22

Peptides

Pilin protein: ABCDEFGHIJKLMNOPQRST

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

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

Pilin protein