SMTL ID : 8xqx.1

Cryo-EM structure of the Ycf2-FtsHi motor complex from chlamydomonas reinhardtii in apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LMG.1: 12 residues within 4Å: Chain A: V.160, W.161, D.162, L.165, W.166, F.169, Q.351, W.354, F.356, L.357 Chain B: R.459 Ligands: SQD.3 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.161, A:D.162, A:L.165, A:F.169, A:F.169 Hydrogen bonds: A:V.160, A:Q.351, A:F.356, A:L.357, B:R.459 LMG.4: 3 residues within 4Å: Chain C: F.471, L.479 Chain N: W.88 No protein-ligand interaction detected (PLIP) LMG.8: 13 residues within 4Å: Chain I: W.206, P.207, R.209, D.210, W.211, G.212, D.213, P.215, W.218, W.219 Chain K: L.221 Ligands: SQD.7, LMG.10 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain K Hydrogen bonds: I:D.210, I:W.211, I:G.212, I:D.213, I:D.213, I:D.213, I:D.213 Hydrophobic interactions: K:L.221 LMG.10: 15 residues within 4Å: Chain I: P.215, M.216, W.219, F.223, I.226, A.316, L.317, G.320, T.324 Chain K: S.219, L.221, V.242, A.243, K.244 Ligands: LMG.8 9 PLIP interactions: 4 interactions with chain I, 5 interactions with chain K Hydrophobic interactions: I:W.219, I:F.223, I:I.226, I:A.316 Hydrogen bonds: K:S.219, K:S.219, K:V.242, K:K.244, K:K.244 LMG.13: 16 residues within 4Å: Chain M: A.354, F.357, K.358, H.361, W.394, V.412, G.414, W.415, V.444, A.453, S.454, G.456, H.457, R.460, L.520, S.524 13 PLIP interactions: 13 interactions with chain M Hydrophobic interactions: M:A.354, M:F.357, M:K.358, M:K.358, M:W.394, M:V.444, M:A.453 Hydrogen bonds: M:V.412, M:G.414 Salt bridges: M:H.457, M:R.460, M:R.460, M:R.460

1 x MG: MAGNESIUM ION

MG.2: 2 residues within 4Å: Chain A: T.506 Chain F: R.709 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.506

3 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

SQD.3: 12 residues within 4Å: Chain A: V.160, W.354, D.355, F.356 Chain B: L.458, R.459, Y.460, V.462, P.463 Chain O: F.458 Chain R: T.49 Ligands: LMG.1 9 PLIP interactions: 5 interactions with chain B, 1 interactions with chain O, 3 interactions with chain A Hydrophobic interactions: B:V.462, O:F.458, A:V.160 Hydrogen bonds: B:R.459, A:D.355, A:F.356 Salt bridges: B:R.459, B:R.459, B:R.459 SQD.7: 12 residues within 4Å: Chain D: F.264 Chain I: W.198, R.200, W.206, W.211, D.213, W.218, G.251, A.255 Chain M: R.468 Ligands: LMG.8, Y01.14 7 PLIP interactions: 5 interactions with chain I, 2 interactions with chain M Hydrophobic interactions: I:W.218, I:A.255 Hydrogen bonds: I:R.200, I:D.213, M:R.468, M:R.468 Salt bridges: I:R.200 SQD.11: 9 residues within 4Å: Chain K: E.135, R.137, F.141, S.142, W.145, Q.149, R.248, F.255 Chain L: W.209 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:F.141, K:F.255, K:F.255 Hydrogen bonds: K:E.135, K:R.137 Salt bridges: K:R.248

2 x DGA: DIACYL GLYCEROL

DGA.5: 22 residues within 4Å: Chain B: L.453, M.457, Y.460, T.461, F.464 Chain D: L.332, W.335, L.336, A.1406, S.1409, L.1410 Chain L: I.235, W.238, L.256, L.257, M.260 Chain O: W.455, W.460 Chain R: F.46, Y.50, L.53, M.325 15 PLIP interactions: 4 interactions with chain D, 6 interactions with chain L, 1 interactions with chain R, 3 interactions with chain B, 1 interactions with chain O Hydrophobic interactions: D:W.335, D:W.335, D:L.336, D:L.336, L:I.235, L:W.238, L:W.238, L:L.256, L:L.256, L:L.257, R:L.53, B:L.453, B:M.457, B:Y.460, O:W.455 DGA.12: 6 residues within 4Å: Chain D: L.344, L.1393, L.1394, L.1401 Chain L: V.236, Y.240 5 PLIP interactions: 1 interactions with chain L, 4 interactions with chain D Hydrophobic interactions: L:V.236, D:L.344, D:L.344, D:L.1393, D:L.1394

2 x Y01: CHOLESTEROL HEMISUCCINATE

Y01.6: 11 residues within 4Å: Chain D: Y.320, F.321, V.322 Chain I: L.334, P.335, W.357 Chain K: W.138, L.140, T.143 Chain L: F.219, F.223 13 PLIP interactions: 3 interactions with chain I, 3 interactions with chain K, 4 interactions with chain D, 3 interactions with chain L Hydrophobic interactions: I:L.334, I:P.335, I:W.357, K:W.138, K:L.140, K:T.143, D:Y.320, D:Y.320, D:Y.320, D:V.322, L:F.219, L:F.219, L:F.223 Y01.14: 10 residues within 4Å: Chain I: W.218 Chain M: W.458, L.459, W.462, G.464, L.465, L.486, A.489, L.493 Ligands: SQD.7 6 PLIP interactions: 5 interactions with chain M, 1 interactions with chain I Hydrophobic interactions: M:W.458, M:L.459, M:W.462, M:L.486, M:A.489, I:W.218

2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

DGD.9: 16 residues within 4Å: Chain I: I.226, M.227, A.229, G.230, G.231, P.243, A.246, G.247, E.287, W.292, H.294, K.295, E.308, L.309, T.310, A.313 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:A.229, I:A.313 Hydrogen bonds: I:M.227, I:G.231, I:W.292, I:K.295, I:L.309, I:T.310 Salt bridges: I:H.294, I:K.295 DGD.15: 12 residues within 4Å: Chain K: P.157, P.158, A.159 Chain L: W.186, Q.187, F.190, Y.195 Chain N: A.82, A.86, F.87, W.88, E.91 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 2 interactions with chain N Hydrogen bonds: K:A.159, L:Q.187, N:E.91, N:E.91

2 x 01: Phytosterol

01.16: 12 residues within 4Å: Chain D: N.736 Chain P: W.255, L.313, V.316, A.317, W.320, A.412, L.413, P.423, L.471, T.472 Ligands: 01.17 9 PLIP interactions: 9 interactions with chain P Hydrophobic interactions: P:W.255, P:V.316, P:A.317, P:W.320, P:W.320, P:W.320, P:P.423, P:L.471, P:L.471 01.17: 13 residues within 4Å: Chain P: L.236, L.305, W.320, L.323, L.324, L.405, L.409, V.445, V.474, V.484, F.488, L.494 Ligands: 01.16 14 PLIP interactions: 14 interactions with chain P Hydrophobic interactions: P:L.236, P:L.305, P:W.320, P:L.323, P:L.324, P:L.324, P:L.409, P:V.445, P:V.474, P:V.484, P:F.488, P:L.494, P:L.494 Hydrogen bonds: P:T.472

2 x ZN: ZINC ION

ZN.18: 4 residues within 4Å: Chain R: C.58, C.61, C.306, C.309 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.58, R:C.61, R:C.306, R:C.309 ZN.19: 4 residues within 4Å: Chain R: C.69, C.72, C.113, C.116 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:C.69, R:C.72, R:C.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, K. et al., Conservation and specialization of the Ycf2-FtsHi chloroplast protein import motor in green algae. Cell (2024)

Release Date

2024-09-11

Peptides

Fhl1: A
Fhl3: BC
Ycf2: D
Ctap1: E
Ctap6: F
ARHL: G
PcyA: H
CrTam39: I
ACP: J
CrTam29: K
CrTam34: L
FADL: M
CrTam15: N
CrTam49: O
Ctap7: P
Tic22: Q
DnaJ: R
CrTam35: S
UNK: T
UNK: U
CrTam31: V

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
U

U
V

V
T

Fhl1

Fhl3

Ycf2

Ctap1

Ctap6

ARHL

PcyA

CrTam39

ACP

CrTam29

CrTam34

FADL

CrTam15

CrTam49

Ctap7

Tic22

DnaJ

CrTam35

UNK

UNK

CrTam31

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