Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8y9y
Q-score: 0.522
Ou X, Ma C, Sun D, Xu J, Wang Y, Wu X, Wang D, Yang S, Gao N, Song C, Li L
Cell (2025)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Protein translocase subunit sece (8 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Substrate ftsq-lacy(+1c) (7 kDa, Protein from Escherichia coli K-12)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Seca-secy complex with the substrate ftsq-lacy(+1c) (Complex from Geobacillus thermodenitrificans NG80-2)
- Beryllium trifluoride ion (66 Da, Ligand)
Structure of the SecA-SecY complex with the substrate HmBRI-3TM
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8y9z
Q-score: 0.453
Ou X, Ma C, Sun D, Xu J, Wang Y, Wu X, Wang D, Yang S, Gao N, Song C, Li L
Cell (2025)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Seca-secy complex with the substrate hmbri-3tm (Complex from Geobacillus thermodenitrificans NG80-2)
- Protein translocase subunit sece (8 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Bacteriorhodopsin-i (11 kDa, Protein from Haloarcula marismortui ATCC 43049)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Nanobody (13 kDa, Protein from Lama glama)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C)
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8ya0
Q-score: 0.515
Ou X, Ma C, Sun D, Xu J, Wang Y, Wu X, Wang D, Yang S, Gao N, Song C, Li L
Cell (2025)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Protein translocase subunit seca (87 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Seca-secy complex with the substrate ftsq-lacy(+7c) (Complex from Geobacillus thermodenitrificans NG80-2)
- Cell division protein ftsq,lactose permease (7 kDa, Protein from Escherichia coli K-12)
- Nanobody (12 kDa, Protein from Lama glama)
- Protein translocase subunit sece (6 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Nanobody (12 kDa, Protein from Lama glama)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Green fluorescent protein (25 kDa, Protein from Aequorea victoria)
- Beryllium trifluoride ion (66 Da, Ligand)
Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C)
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 8ya2
Q-score: 0.343
Ou X, Ma C, Sun D, Xu J, Wang Y, Wu X, Wang D, Yang S, Gao N, Song C, Li L
Cell (2025)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Protein translocase subunit sece (8 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Cell division protein ftsq,lactose permease (8 kDa, Protein from Escherichia coli K-12)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Seca-secy complex with the substrate ftsq-lacy(+20c) (Complex from Geobacillus thermodenitrificans NG80-2)
- Nanobody (12 kDa, Protein from Lama glama)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Green fluorescent protein (25 kDa, Protein from Aequorea victoria)
- Beryllium trifluoride ion (66 Da, Ligand)
Structure of the SecA-SecY complex with the substrate HmBRI-7TM
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 8yas
Q-score: 0.29
Ou X, Ma C, Sun D, Xu J, Wang Y, Wu X, Wang D, Yang S, Gao N, Song C, Li L
Cell (2025)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Protein translocase subunit sece (8 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Seca-secy complex with the substrate hmbri-7tm (Complex from Geobacillus thermodenitrificans NG80-2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8znz
Q-score: 0.547
Xu JG, Chen S, He Y, Zhu X, Wang Y, Ye Z, Zhou JC, Wu X, Zhang L, Ren X, Jia H, Yu H, Wei X, Feng Y, Chen X, Cui X, Pan X, Wang S, Xia S, Shang H, Pu Y, Xu W, Li H, Chen Q, Chen Z, Wang M, Yan X, Shi H, Li M, Xia Y, Bellelli R, Dong S, He J, Huang J, Cai CL, Zhu X, Zhan Y, Wan L
Nat Commun (2024) 15 pp. 10872-10872 [ DOI: doi:10.1038/s41467-024-55207-9 Pubmed: 39738003 ]
- Zinc ion (65 Da, Ligand)
- Hb0038 fab light chain (11 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Hb0038 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Hb0039 fab light chain (11 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Hb0039 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Cd73 complexed with hb0017 antibody coaktail (630 kDa, Complex from Homo sapiens)
- 5'-nucleotidase (58 kDa, Protein from Homo sapiens)
Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 8xxv
Q-score: 0.479
Xu J, Xu Y, Hou L, He X, Li Y, Zhao J, Meng X, Wang JJ, Wu Y, Zhang H, Li Y, Hu W, Yuan Q, Wu K, Cheng X, Jiang Y, Xia Y, Xu HE, Wu C
PNAS (2024) 121 pp. e2403304121-e2403304121 [ DOI: doi:10.1073/pnas.2403304121 Pubmed: 39665758 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (26 kDa, Protein from Mus musculus)
- [(2~{r})-1-hexadecanoyloxy-3-[oxidanyl-[(2~{s},3~{r},5~{r},6~{s})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (~{z})-octadec-9-enoate (837 Da, Ligand)
- Prostaglandin d2 receptor 2 (38 kDa, Protein from Homo sapiens)
- Indomethacin (357 Da, Ligand)
- Pd2r2-indomethacin-g protein (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
Cryo-EM Structure of the Prostaglandin D2 Receptor 2-PGD2 Coupled to G Protein
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 9iyb
Q-score: 0.475
Xu J, Xu Y, Hou L, He X, Li Y, Zhao J, Meng X, Wang JJ, Wu Y, Zhang H, Li Y, Hu W, Yuan Q, Wu K, Cheng X, Jiang Y, Xia Y, Xu HE, Wu C
PNAS (2024) 121 pp. e2403304121-e2403304121 [ DOI: doi:10.1073/pnas.2403304121 Pubmed: 39665758 ]
- Prostaglandin d2 receptor 2-pgd2-g protein complex (160 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (26 kDa, Protein from Rattus norvegicus)
- [(2~{r})-1-hexadecanoyloxy-3-[oxidanyl-[(2~{s},3~{r},5~{r},6~{s})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (~{z})-octadec-9-enoate (837 Da, Ligand)
- Prostaglandin d2 receptor 2 (43 kDa, Protein from Homo sapiens)
- Prostaglandin d2 (352 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8top
Q-score: 0.391
Wang H, Cheng C, Dal Santo JL, Shen CH, Bylund T, Henry AR, Howe CA, Hwang J, Morano NC, Morris DJ, Pletnev S, Roark RS, Zhou T, Hansen BT, Hoyt FH, Johnston TS, Wang S, Zhang B, Ambrozak DR, Becker JE, Bender MF, Changela A, Chaudhary R, Corcoran M, Corrigan AR, Foulds KE, Guo Y, Lee M, Li Y, Lin BC, Liu T, Louder MK, Mandolesi M, Mason RD, McKee K, Nair V, O'Dell S, Olia AS, Ou L, Pegu A, Raju N, Rawi R, Roberts-Torres J, Sarfo EK, Sastry M, Schaub AJ, Schmidt SD, Schramm CA, Schwartz CL, Smith SC, Stephens T, Stuckey J, Teng IT, Todd JP, Tsybovsky Y, Van Wazer DJ, Wang S, Doria-Rose NA, Fischer ER, Georgiev IS, Karlsson Hedestam GB, Sheng Z, Woodward RA, Douek DC, Koup RA, Pierson TC, Shapiro L, Shaw GM, Mascola JR, Kwong PD
Cell (2024) 187 pp. 7214-7231.e23 [ Pubmed: 39471811 DOI: doi:10.1016/j.cell.2024.10.003 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of antibody gpz6-b.01 (23 kDa, Protein from Macaca mulatta)
- Heavy chain of antibody gpz6-b.01 (25 kDa, Protein from Macaca mulatta)
- Hiv-1 bg505 ds-sosip glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Complex between hiv-1 env bg505 ds-sosip and antibody gpz6-b.01 (720 kDa, Complex from Homo sapiens)
- Hiv-1 bg505 ds-sosip gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 8j0s
Q-score: 0.592
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ Pubmed: 38961288 DOI: doi:10.1038/s41586-024-07605-8 ]
- Mycobacterium tuberculosis atp synthase in complex with bedaquiline(bdq) (Complex from Mycobacterium tuberculosis)
- Atp synthase subunit b (18 kDa, Protein from Mycobacterium tuberculosis)
- Multifunctional fusion protein (48 kDa, Protein from Mycobacterium tuberculosis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit c (8 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit beta (53 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit a (27 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase epsilon chain (13 kDa, Protein from Mycobacterium tuberculosis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase gamma chain (33 kDa, Protein from Mycobacterium tuberculosis)
- Bedaquiline (555 Da, Ligand)
- Atp synthase subunit alpha (59 kDa, Protein from Mycobacterium tuberculosis)