Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-.
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7xha
Q-score: 0.46
Dong L, Yang S, Chen J, Wu X, Sun D, Song C, Li L
PNAS (2023) 120 pp. e2208070120-e2208070120 [ Pubmed: 36598944 DOI: doi:10.1073/pnas.2208070120 ]
- Sece (Complex from Escherichia coli)
- Seca (Complex from Geobacillus thermodenitrificans NG80-2)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Complex of the seca/secye/proompa(4y)-sfgfp with adp.bef3- (180 kDa, Complex from Bacillus subtilis subsp. subtilis str. 168)
- Sfgfp (Complex)
- Beryllium trifluoride ion (66 Da, Ligand)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Translocating polypeptide (33 kDa, Protein from Escherichia coli)
- Secy (Complex from Geobacillus thermodenitrificans NG80-2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Protein translocase subunit sece (7 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7xhb
Q-score: 0.429
Dong L, Yang S, Chen J, Wu X, Sun D, Song C, Li L
PNAS (2023) 120 pp. e2208070120-e2208070120 [ Pubmed: 36598944 DOI: doi:10.1073/pnas.2208070120 ]
- Translocating peptide (37 kDa, Protein from Escherichia coli)
- Sece (Complex from Escherichia coli)
- Seca (Complex from Geobacillus thermodenitrificans NG80-2)
- Complex of the seca/secye/proompa(4y)-sfgfp with adp. (180 kDa, Complex from Bacillus subtilis subsp. subtilis str. 168)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Sfgfp (Complex)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Secy (Complex from Geobacillus thermodenitrificans NG80-2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Protein translocase subunit sece (7 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
Ribosome-bound SecYEG translocon in a nanodisc
Resolution: 6.0 Å
EM Method: Single-particle
Fitted PDBs: 6r7l
Q-score: 0.245
Kater L, Frieg B, Berninghausen O, Gohlke H, Beckmann R, Kedrov A
EMBO Rep (2019) 20 pp. e48191-e48191 [ DOI: doi:10.15252/embr.201948191 Pubmed: 31379073 ]
- Secg (1 kDa, Protein from Escherichia coli)
- Sece,protein translocase subunit sece,protein translocase subunit sece,protein translocase subunit sece (10 kDa, Protein from Escherichia coli)
- Stalled e. coli ribosome nascent chain complex (rnc) bound to the translocon secyeg in a nanodisc (Complex from Escherichia coli)
- Protein translocase subunit secy (48 kDa, Protein from Escherichia coli)
Structure of a substrate engaged SecA-SecY protein translocation machine
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 6itc
Q-score: 0.436
Ma C, Wu X, Sun D, Park E, Catipovic MA, Rapoport TA, Gao N, Li L
Nat Commun (2019) 10 pp. 2872-2872 [ DOI: doi:10.1038/s41467-019-10918-2 Pubmed: 31253804 ]
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis (strain 168))
- Protein translocase subunit sece (8 kDa, Protein from Geobacillus thermodenitrificans (strain NG80-2))
- Seca-secy complex (Complex from Bacillus subtilis)
- Translocating peptide (6 kDa, Protein from Escherichia coli)
- Protein translocase subunit secy (46 kDa, Protein from Geobacillus thermodenitrificans (strain NG80-2))
- Beryllium trifluoride ion (66 Da, Ligand)
- Green fluorescent protein (26 kDa, Protein from Aequorea victoria)
- Nanobody (12 kDa, Protein from Lama glama)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Nanobody (12 kDa, Protein from Lama glama)
cryoEM structure of bacterial holo-translocon
Resolution: 14.0 Å
EM Method: Single-particle
Fitted PDBs: 5mg3
Q-score: 0.034
Botte M, Zaccai NR, Nijeholt JL, Martin R, Knoops K, Papai G, Zou J, Deniaud A, Karuppasamy M, Jiang Q, Roy AS, Schulten K, Schultz P, Rappsilber J, Zaccai G, Berger I, Collinson I, Schaffitzel C
Sci Rep (2016) 6 pp. 38399-38399 [ Pubmed: 27924919 DOI: doi:10.1038/srep38399 ]
- Protein translocase subunit secy (50 kDa, Protein from Escherichia coli)
- Bacterial holo-translocon (htl) (250 kDa, Complex from Escherichia coli)
- Protein translocase subunit secf (35 kDa, Protein from Escherichia coli)
- Membrane protein insertase yidc (62 kDa, Protein from Escherichia coli)
- Protein translocase subunit sece (15 kDa, Protein from Escherichia coli)
- Protein translocase subunit secd (67 kDa, Protein from Escherichia coli)
- Protein-export membrane protein secg (14 kDa, Protein from Escherichia coli)
Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 5nco
Q-score: 0.218
Jomaa A, Fu YH, Boehringer D, Leibundgut M, Shan SO, Ban N
Nat Commun (2017) 8 pp. 15470-15470 [ Pubmed: 28524878 DOI: doi:10.1038/ncomms15470 ]
- Signal recognition particle receptor ftsy (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- Protein translocase subunit secy (45 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Srp, sr, and secyeg (Complex from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Signal sequence (1a9l) (2 kDa, Protein from Escherichia coli)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- Protein translocase subunit sece (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
- P-site trna-cca end (894 Da, RNA from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Ribosome (Complex from Escherichia coli)
- Ribosome nascent chain, srp, sr, and secyeg quaternary complex (2 MDa, Complex)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- Signal recognition particle protein,signal recognition particle protein,signal recognition particle protein,signal recognition particle protein,signal recognition particle protein,signal recognition particle protein,signal recognition particle protein,signal recognition particle protein,signal recognition particle protein,signal recognition particle protein (48 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 4.5s srp rna (ffs) (33 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- Protein-export membrane protein secg (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
RNC in complex with a translocating SecYEG
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 5gae
Q-score: 0.441
Jomaa A, Boehringer D, Leibundgut M, Ban N
Nat Commun (2016) 7 pp. 10471-10471 [ Pubmed: 26804923 DOI: doi:10.1038/ncomms10471 ]
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Protein translocase subunit sece (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Ribosome nascent chain secyeg complex (2 MDa, Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Protein translocase subunit secy (48 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- Secg (2 kDa, Protein from Escherichia coli)
- Trna cca end (5'-r(p*cp*cp*a)-3') (894 Da, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)