SMTL ID : 6itc.1

Structure of a substrate engaged SecA-SecY protein translocation machine

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.107, E.208 Ligands: BEF.2, ADP.3 No protein-ligand interaction detected (PLIP)

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.2: 11 residues within 4Å: Chain A: T.102, G.103, E.208, R.489, G.490, Q.521, G.524, R.525, R.528 Ligands: MG.1, ADP.3 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 17 residues within 4Å: Chain A: M.79, F.80, P.81, F.82, Q.85, T.102, G.103, E.104, G.105, K.106, T.107, D.492, K.494, R.528, Q.529 Ligands: MG.1, BEF.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.80, A:Q.85, A:G.103, A:G.105, A:K.106, A:T.107, A:T.107, A:T.107, A:D.492 Salt bridges: A:K.106, A:R.528

2 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.4: 3 residues within 4Å: Chain B: R.356 Chain C: R.3, F.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.7 Salt bridges: B:R.356, B:R.360 PGV.5: 15 residues within 4Å: Chain B: C.60, G.186, I.187, G.190, I.191, I.194, V.214, A.215, V.218, Q.390, I.391, S.395, L.396 Chain C: V.37 Chain E: G.28 9 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: B:I.191, B:V.214, B:A.215, B:V.218, B:I.391, C:V.37, C:V.37 Hydrogen bonds: B:S.395, E:G.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, C. et al., Structure of the substrate-engaged SecA-SecY protein translocation machine. Nat Commun (2019)

Release Date

2019-06-12

Peptides

Protein translocase subunit SecA: A
Protein translocase subunit SecY: B
Protein translocase subunit SecE: C
Nanobody: D
Translocating peptide: E
Green fluorescent protein: F
Nanobody: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
Y

C
E

D
V

E
B

F
G

G
C

Membrane

We predict this structure to be a membrane protein.
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Protein translocase subunit SecA

Protein translocase subunit SecY

Protein translocase subunit SecE

Nanobody

Translocating peptide

Green fluorescent protein

Nanobody

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