SMTL ID : 8xqw.1

Cryo-EM structure of the Ycf2-FtsHi motor complex from Chlamydomonas reinhardtii in AMPPNP bound 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: 10 residues within 4Å: Chain A: V.160, D.162, L.165, W.166, F.169, Q.351, W.354, F.356 Chain B: R.459 Ligands: SQD.4 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.162, A:L.165, A:W.166, A:F.169, A:F.169 Hydrogen bonds: A:V.160, A:Q.351, A:F.356, B:R.459 LMG.5: 3 residues within 4Å: Chain C: I.474, L.479 Ligands: DGD.16 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.474 LMG.12: 12 residues within 4Å: Chain I: W.206, P.207, R.209, W.211, G.212, D.213, P.215, W.218, W.219 Chain K: L.221 Ligands: SQD.11, LMG.14 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: I:W.218, K:L.221 Hydrogen bonds: I:W.211, I:G.212, I:D.213, I:D.213, I:D.213 LMG.14: 12 residues within 4Å: Chain I: P.215, M.216, W.219, I.226, A.316, L.317, G.320, T.324 Chain K: S.219, L.221, K.244 Ligands: LMG.12 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain I Hydrogen bonds: K:K.244 Hydrophobic interactions: I:W.219, I:I.226 LMG.17: 17 residues within 4Å: Chain M: A.354, F.357, K.358, V.412, G.414, W.415, H.416, V.444, A.453, S.454, G.456, H.457, R.460, L.514, L.520, S.524, M.571 13 PLIP interactions: 13 interactions with chain M Hydrophobic interactions: M:F.357, M:K.358, M:V.444, M:A.453, M:L.514 Hydrogen bonds: M:V.412, M:G.414, M:H.416, M:R.460, M:R.460 Salt bridges: M:H.457, M:R.460, M:R.460

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

ANP.2: 18 residues within 4Å: Chain A: I.461, A.462, G.463, M.464, P.501, G.502, T.503, G.504, K.505, T.506, Y.507, H.643, A.669, A.670, A.673 Chain F: R.706, R.709 Ligands: MG.3 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:A.462, A:A.462, A:G.502, A:T.503, A:T.503, A:G.504, A:K.505, A:K.505, A:T.506, A:T.506, A:T.506, A:Y.507, A:N.607, F:R.706, F:R.709 Salt bridges: F:R.706 ANP.6: 10 residues within 4Å: Chain C: A.568, P.569, G.570, T.571, G.572, D.626, I.703, G.731, A.732 Chain D: R.2333 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.570, C:T.571, C:G.572, D:R.2333 ANP.9: 13 residues within 4Å: Chain C: R.682 Chain E: A.439, P.478, G.479, T.480, G.481, K.482, T.483, I.615, H.619, G.643, A.644, A.647 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:A.439, E:G.479, E:T.480, E:T.480, E:G.481, E:K.482, E:K.482, E:K.482, E:T.483, E:T.483, E:T.483, E:T.483, C:R.682 Salt bridges: C:R.682 ANP.10: 11 residues within 4Å: Chain F: I.551, A.552, N.554, P.591, G.592, N.593, G.594, K.595, T.596, L.597, H.731 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:A.552, F:A.552, F:N.554, F:G.592, F:G.594, F:K.595, F:T.596

1 x MG: MAGNESIUM ION

MG.3: 3 residues within 4Å: Chain A: T.506, D.558 Ligands: ANP.2 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.4: 11 residues within 4Å: Chain A: V.160, W.354, D.355, F.356 Chain B: R.459, Y.460, V.462, P.463, V.466 Chain R: T.49 Ligands: LMG.1 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.355, A:F.356, B:R.459 Salt bridges: B:R.459, B:R.459, B:R.459 SQD.11: 12 residues within 4Å: Chain I: W.198, R.200, W.206, W.211, D.213, W.218, L.221, G.251, A.255 Chain M: R.468 Ligands: LMG.12, Y01.18 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain M Hydrophobic interactions: I:W.218, I:L.221, I:A.255 Hydrogen bonds: I:R.200, I:D.213, M:R.468 Salt bridges: I:R.200 SQD.15: 8 residues within 4Å: Chain K: E.135, R.137, F.141, W.145, R.248, L.254, F.255 Chain L: W.209 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:F.141, K:F.141, K:W.145, K:L.254, K:F.255, K:F.255 Hydrogen bonds: K:E.135 Salt bridges: K:R.248

2 x DGA: DIACYL GLYCEROL

DGA.7: 8 residues within 4Å: Chain D: L.337, L.344, L.1393, L.1394, S.1397, L.1401 Chain L: V.236, Y.240 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D Hydrophobic interactions: L:V.236, D:L.1394 DGA.19: 23 residues within 4Å: Chain B: L.453, M.457, T.461, F.464 Chain D: L.332, W.335, L.336, V.339, A.1406, S.1409, L.1410 Chain L: V.234, I.235, W.238, P.253, L.256, M.260 Chain O: W.455, V.459, W.460 Chain R: Y.50, L.53, M.325 11 PLIP interactions: 4 interactions with chain L, 5 interactions with chain D, 1 interactions with chain B, 1 interactions with chain O Hydrophobic interactions: L:V.234, L:I.235, L:W.238, L:P.253, D:L.332, D:W.335, D:W.335, D:L.336, D:V.339, B:T.461, O:V.459

2 x Y01: CHOLESTEROL HEMISUCCINATE

Y01.8: 11 residues within 4Å: Chain D: Y.320, F.321, V.322 Chain I: L.334, P.335, W.357 Chain K: L.140, T.143 Chain L: F.219, W.220, F.223 11 PLIP interactions: 4 interactions with chain D, 4 interactions with chain L, 3 interactions with chain I Hydrophobic interactions: D:Y.320, D:Y.320, D:Y.320, D:V.322, L:F.219, L:F.219, L:W.220, L:F.223, I:L.334, I:L.334, I:W.357 Y01.18: 9 residues within 4Å: Chain M: W.458, L.459, S.461, W.462, G.464, L.486, A.489, L.493 Ligands: SQD.11 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:W.458, M:W.462, M:W.462, M:L.486, M:A.489, M:L.493

2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

DGD.13: 15 residues within 4Å: Chain I: I.226, M.227, A.229, G.230, G.231, T.234, P.243, G.247, E.287, W.292, H.294, K.295, E.308, L.309, T.310 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:A.229, I:L.309 Hydrogen bonds: I:M.227, I:T.234, I:G.247, I:E.287, I:K.295, I:L.309, I:T.310, I:T.310 Salt bridges: I:H.294, I:K.295 DGD.16: 12 residues within 4Å: Chain K: P.158, A.159 Chain L: V.183, W.186, Q.187, F.190, Y.195 Chain N: A.82, A.86, F.87, E.91 Ligands: LMG.5 5 PLIP interactions: 2 interactions with chain L, 2 interactions with chain N, 1 interactions with chain K Hydrophobic interactions: L:W.186, N:A.82 Hydrogen bonds: L:Q.187, N:E.91, K:A.159

2 x 01: Phytosterol

01.20: 14 residues within 4Å: Chain D: N.736, I.737 Chain P: W.255, L.313, V.316, A.317, W.320, L.413, P.423, W.437, V.443, L.471, T.472 Ligands: 01.21 17 PLIP interactions: 16 interactions with chain P, 1 interactions with chain D Hydrophobic interactions: P:W.255, P:L.313, P:V.316, P:V.316, P:A.317, P:W.320, P:W.320, P:L.413, P:L.413, P:L.413, P:L.413, P:P.423, P:W.437, P:V.443, P:L.471, P:L.471, D:I.737 01.21: 12 residues within 4Å: Chain P: L.236, L.305, W.320, L.324, L.405, L.409, V.445, V.474, V.484, F.488, L.494 Ligands: 01.20 14 PLIP interactions: 14 interactions with chain P Hydrophobic interactions: P:L.236, P:L.305, P:W.320, P:W.320, P:W.320, P:L.324, P:L.324, P:L.405, P:L.409, P:V.445, P:V.474, P:V.484, P:F.488, P:L.494

2 x ZN: ZINC ION

ZN.22: 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.23: 4 residues within 4Å: Chain R: C.69, C.72, C.113, C.116 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.69, R:C.72, R:C.113, 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

Membrane

We predict this structure to be a membrane protein.
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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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