SMTL ID : 7xzi.1

Cryo-EM structure of TOC-TIC supercomplex from Chlamydomonas reinhardtii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.77 Å

Oligo State

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

Ligands

5 x AJP: Digitonin(Non-covalent)

AJP.1: 1 residues within 4Å: Chain B: H.270 No protein-ligand interaction detected (PLIP) AJP.2: 7 residues within 4Å: Chain C: L.63, R.64, W.67 Chain M: G.11, D.15, V.18, T.21 12 PLIP interactions: 4 interactions with chain M, 8 interactions with chain C Hydrophobic interactions: M:V.18, C:R.64, C:W.67, C:W.67, C:W.67, C:W.67, C:W.67 Hydrogen bonds: M:G.11, M:D.15, M:D.15, C:R.64 Salt bridges: C:R.64 AJP.18: 8 residues within 4Å: Chain G: W.105, M.108, A.161, I.166, N.169, K.171, I.172 Ligands: LHG.17 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:W.105, G:A.161, G:I.166, G:I.166, G:I.172 Hydrogen bonds: G:N.169, G:K.171 AJP.21: 5 residues within 4Å: Chain G: T.196, N.199 Chain I: K.91, F.95, F.98 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:K.91, I:F.95, I:F.98, I:F.98 Hydrogen bonds: I:K.91, G:T.196 AJP.23: 7 residues within 4Å: Chain G: L.164, R.168, G.258 Chain I: P.136, L.137, F.138, G.139 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:L.137

5 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.3: 12 residues within 4Å: Chain C: L.77, V.78, S.81, F.82, R.85, S.86, N.88, W.89, F.90, K.112 Chain F: E.361 Ligands: LMG.12 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.77, C:V.78, C:F.82, C:F.82, C:W.89, C:F.90 Hydrogen bonds: C:R.85, C:N.88 Salt bridges: C:K.112 LMG.11: 20 residues within 4Å: Chain F: I.179, Y.182, L.183, G.185, F.186, L.189, E.223, Q.224, A.320, S.323, I.324, L.329, T.332, I.333 Chain G: F.140, I.226, L.229 Chain H: T.35, V.55 Ligands: LHG.19 13 PLIP interactions: 9 interactions with chain F, 3 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: F:I.179, F:F.186, F:L.329, F:I.333, G:F.140, G:I.226, G:L.229, H:T.35 Hydrogen bonds: F:R.181, F:G.185, F:F.186, F:Q.224, F:S.323 LMG.12: 19 residues within 4Å: Chain C: L.77, S.81, H.84 Chain F: L.329, I.333, T.360, E.361, T.362, A.363, F.364, S.374, Q.395, F.1911 Chain G: W.136, Y.139, F.140, E.142 Ligands: LMG.3, LMG.13 16 PLIP interactions: 8 interactions with chain F, 4 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: F:L.329, F:I.333, F:E.361, F:T.362, F:F.364, F:F.1911, G:W.136, G:F.140, G:F.140 Hydrogen bonds: F:S.374, F:Q.395, G:E.142, C:H.84 Salt bridges: C:H.84, C:H.84, C:H.84 LMG.13: 12 residues within 4Å: Chain F: L.9, Y.16, V.17, N.31, Y.32, T.33, V.38, Y.41, S.45, L.358, L.1918 Ligands: LMG.12 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:L.9, F:Y.16, F:Y.16, F:V.17, F:V.38, F:Y.41, F:L.358 Hydrogen bonds: F:N.31, F:Y.32, F:T.33, F:T.33 LMG.14: 11 residues within 4Å: Chain G: F.159, G.246, L.249, Q.250, Q.253 Chain I: V.101, S.104, W.105, L.141, D.142, F.143 9 PLIP interactions: 4 interactions with chain G, 5 interactions with chain I Hydrophobic interactions: G:F.159, I:W.105, I:W.105, I:W.105 Hydrogen bonds: G:G.246, G:Q.253, G:Q.253, I:D.142, I:D.142

1 x R16: HEXADECANE(Non-functional Binders)

R16.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

7 x D12: DODECANE(Non-functional Binders)(Non-covalent)

D12.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.8: 3 residues within 4Å: Chain F: L.59, W.174 Ligands: D12.9 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.59, F:W.174 D12.9: 2 residues within 4Å: Chain F: F.58 Ligands: D12.8 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.58 D12.10: 1 residues within 4Å: Chain F: F.50 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.50 D12.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.16: 2 residues within 4Å: Chain G: F.213, L.216 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.213 D12.22: 1 residues within 4Å: Chain I: S.108 No protein-ligand interaction detected (PLIP)

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.6: 14 residues within 4Å: Chain E: H.770, R.802, K.807 Chain F: W.1235, K.1238, I.1242, E.1273, K.1276, Y.1359, K.1457, K.1464, S.1690, L.1691, K.1692 18 PLIP interactions: 3 interactions with chain E, 15 interactions with chain F Hydrogen bonds: E:K.807, F:Y.1359, F:Y.1359, F:S.1690, F:S.1690, F:L.1691 Salt bridges: E:R.802, E:K.807, F:K.1238, F:K.1238, F:K.1276, F:K.1276, F:K.1457, F:K.1457, F:K.1464, F:K.1464, F:K.1692, F:K.1692

5 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.7: 10 residues within 4Å: Chain F: F.157, L.158, G.166, W.167, R.168, F.169, F.170, W.174, Y.251 Chain H: R.74 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain H Hydrophobic interactions: F:F.157, F:L.158, F:W.167, F:W.167, F:W.167, F:F.169, F:F.170, F:F.170, F:W.174 Hydrogen bonds: F:G.166, F:R.168, F:R.168, F:R.168, H:R.74, H:R.74, H:E.75 Salt bridges: H:R.74 LHG.17: 5 residues within 4Å: Chain G: T.102, W.103, P.104, M.108 Ligands: AJP.18 No protein-ligand interaction detected (PLIP) LHG.19: 12 residues within 4Å: Chain C: K.61, L.62, G.65, G.66, L.69 Chain F: F.180, L.183, V.190, W.194 Chain G: F.230, W.236 Ligands: LMG.11 7 PLIP interactions: 1 interactions with chain G, 4 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: G:F.230, F:F.180, F:L.183, F:V.190, F:W.194, C:L.62, C:L.69 LHG.20: 15 residues within 4Å: Chain F: N.838, R.839, L.841 Chain G: F.127, R.130, P.208, W.209, L.212, A.215 Chain H: N.36, L.39, L.40, M.43, W.126, Q.127 8 PLIP interactions: 1 interactions with chain F, 5 interactions with chain G, 2 interactions with chain H Hydrogen bonds: F:R.839, G:W.209, H:Q.127 Hydrophobic interactions: G:F.127, G:F.127, G:A.215, H:L.39 Salt bridges: G:R.130 LHG.24: 3 residues within 4Å: Chain F: Y.228 Chain H: F.49 Chain K: W.209 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Architecture of chloroplast TOC-TIC translocon supercomplex. Nature (2023)

Release Date

2023-01-11

Peptides

Ctap3: A
Ctap4: B
Ctap5: C
Toc75: D
Toc90: E
Tic214: F
Protein TIC 20: G
Tic15: H
Simp3: I
Tic100: J
Tic56: K
Toc34: L
Simp2: M
Unknown peptide: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

B
4

C
5

D
7

E
9

F
A

G
B

H
C

I
D

J
E

K
F

L
G

M
U

N
X

Membrane

We predict this structure to be a membrane protein.
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Ctap3

Ctap4

Ctap5

Toc75

Toc90

Tic214

Protein TIC 20

Tic15

Simp3

Tic100

Tic56

Toc34

Simp2

Unknown peptide

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