KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(CTD)/Gbeta1gamma2
Nguyen DM, Rath DH, Devost D, Petrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hebert TE, Prive GG
PNAS (2024) 121 pp. e2315018121-e2315018121 [ Pubmed: 38625940 DOI: doi:10.1073/pnas.2315018121 ]
- Gbg2_human (Protein from Homo sapiens)
- Kctd5_human (Protein from Homo sapiens)
- Complex of substrate adaptor kctd5 with cullin-3 and substrate gbeta-gamma (Complex from Homo sapiens)
- Gbb1_human (Protein from Homo sapiens)
KCTD5/Cullin3/Gbeta1gamma2 Complex State A: Composite Map from RELION Multi-body Refinement
Resolution: 3.82 Å
EM Method: Single-particle
Fitted PDBs: 8u81
Q-score: 0.228
Nguyen DM, Rath DH, Devost D, Petrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hebert TE, Prive GG
PNAS (2024) 121 pp. e2315018121-e2315018121 [ Pubmed: 38625940 DOI: doi:10.1073/pnas.2315018121 ]
- Gbg2_human (Protein from Homo sapiens)
- Cullin3 1-381 (Protein from Homo sapiens)
- Kctd5_human (Protein from Homo sapiens)
- Complex of substrate adaptor kctd5 with cullin-3 and substrate gbeta-gamma (Complex from Homo sapiens)
- Gbb1_human (Protein from Homo sapiens)
KCTD5/Cullin3/Gbeta1gamma2 Complex State A: Reference Map for Composite Map EMD-41996
Nguyen DM, Rath DH, Devost D, Petrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hebert TE, Prive GG
PNAS (2024) 121 pp. e2315018121-e2315018121 [ Pubmed: 38625940 DOI: doi:10.1073/pnas.2315018121 ]
- Kctd5 (Protein from Homo sapiens)
- Gbg2_human (Protein from Homo sapiens)
- Cullin3 1-381 (Protein from Homo sapiens)
- Complex of substrate adaptor kctd5 with cullin-3 and substrate gbeta-gamma (Complex from Homo sapiens)
- Gbb1_human (Protein from Homo sapiens)
KCTD5/Cullin3/Gbeta1gamma2 Complex State B: Composite Map from RELION Multi-body Refinement
Resolution: 3.83 Å
EM Method: Single-particle
Fitted PDBs: 8u82
Q-score: 0.254
Nguyen DM, Rath DH, Devost D, Petrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hebert TE, Prive GG
PNAS (2024) 121 pp. e2315018121-e2315018121 [ Pubmed: 38625940 DOI: doi:10.1073/pnas.2315018121 ]
- Gbg2_human (Protein from Homo sapiens)
- Kctd5_human (Protein from Homo sapiens)
- Cullin3 1-381 (Protein from Homo sapiens)
- Complex of substrate adaptor kctd5 with cullin-3 and substrate gbeta-gamma (Complex from Homo sapiens)
- Gbb1_human (Protein from Homo sapiens)
KCTD5/Cullin3/Gbeta1gamma2 Complex State B: Reference Map for Composite Map EMD-42000
Nguyen DM, Rath DH, Devost D, Petrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hebert TE, Prive GG
PNAS (2024) 121 pp. e2315018121-e2315018121 [ Pubmed: 38625940 DOI: doi:10.1073/pnas.2315018121 ]
- Gbg2_human (Protein from Homo sapiens)
- Kctd5_human (Protein from Homo sapiens)
- Cullin3 1-381 (Protein from Homo sapiens)
- Complex of substrate adaptor kctd5 with cullin-3 and substrate gbeta-gamma (Complex from Homo sapiens)
- Gbb1_human (Protein from Homo sapiens)
KCTD5/Cullin3/Gbeta1gamma2 Complex State C: Composite Map from RELION Multi-body Refinement
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 8u83
Q-score: 0.197
Nguyen DM, Rath DH, Devost D, Petrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hebert TE, Prive GG
PNAS (2024) 121 pp. e2315018121-e2315018121 [ Pubmed: 38625940 DOI: doi:10.1073/pnas.2315018121 ]
- Gbg2_human (Protein from Homo sapiens)
- Kctd5_human (Protein from Homo sapiens)
- Cullin3 1-381 (Protein from Homo sapiens)
- Complex of substrate adaptor kctd5 with cullin-3 and substrate gbeta-gamma (Complex from Homo sapiens)
- Gbb1_human (Protein from Homo sapiens)
KCTD5/Cullin3/Gbeta1gamma2 Complex State D: Composite Map from RELION Multi-body Refinement
Resolution: 3.88 Å
EM Method: Single-particle
Fitted PDBs: 8u84
Q-score: 0.227
Nguyen DM, Rath DH, Devost D, Petrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hebert TE, Prive GG
PNAS (2024) 121 pp. e2315018121-e2315018121 [ Pubmed: 38625940 DOI: doi:10.1073/pnas.2315018121 ]
- Gbg2_human (Protein from Homo sapiens)
- Kctd5_human (Protein from Homo sapiens)
- Cullin3 1-381 (Protein from Homo sapiens)
- Complex of substrate adaptor kctd5 with cullin-3 and substrate gbeta-gamma (Complex from Homo sapiens)
- Gbb1_human (Protein from Homo sapiens)
The F1 region of ammocidin-bound Saccharomyces cerevisiae ATP synthase
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7md2
Q-score: 0.52
Reisman BJ, Guo H, Ramsey HE, Wright MT, Reinfeld BI, Ferrell PB, Sulikowski GA, Rathmell WK, Savona MR, Plate L, Rubinstein JL, Bachmann BO
bioRxiv (2021) [ DOI: doi:10.1101/2021.05.31.445492 ]
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit epsilon, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- (3~{e},5~{z},7~{e},9~{r},10~{s},11~{e},13~{e},15~{e},17~{r},18~{s},20~{s})-20-[(1~{r})-1-[(2~{s},3~{r},4~{r},5~{s},6~{r})-5-[(2~{s},4~{s},5~{s},6~{r})-5-[(2~{s},4~{r},5~{r},6~{r})-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-methyl-4-oxidanyl-oxan-2-yl]oxy-3-methoxy-6-(3-methoxypropyl)-5-methyl-2,4-bis(oxidanyl)oxan-2-yl]ethyl]-5,18-dimethoxy-3,7,9,11,13,15-hexamethyl-10-[(2~{r},3~{s},4~{r},5~{r},6~{s})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13,15-hexaen-2-one (1 kDa, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- The f1 region of ammocidin-bound saccharomyces cerevisiae atp synthase (400 kDa, Complex from Saccharomyces cerevisiae)
- Atp synthase subunit gamma (30 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit beta (51 kDa, Protein from Saccharomyces cerevisiae)
The F1 region of apoptolidin-bound Saccharomyces cerevisiae ATP synthase
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7md3
Q-score: 0.46
Reisman BJ, Guo H, Ramsey HE, Wright MT, Reinfeld BI, Ferrell PB, Sulikowski GA, Rathmell WK, Savona MR, Plate L, Rubinstein JL, Bachmann BO
bioRxiv (2021) [ DOI: doi:10.1101/2021.05.31.445492 ]
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit epsilon, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- The f1 region of apoptolidin-bound saccharomyces cerevisiae atp synthase (400 kDa, Complex from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- (3~{e},5~{e},7~{e},9~{r},10~{r},11~{e},13~{e},17~{s},18~{s},20~{s})-18-methoxy-20-[(~{r})-[(2~{r},3~{r},4~{s},5~{r},6~{r})-6-[(2~{r})-3-methoxy-2-[(2~{r},4~{s},5~{s},6~{s})-5-[(2~{s},4~{r},5~{r},6~{r})-4-methoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4,6-dimethyl-4-oxidanyl-oxan-2-yl]oxy-propyl]-3,5-dimethyl-2,4-bis(oxidanyl)oxan-2-yl]-oxidanyl-methyl]-10-[(2~{r},3~{s},4~{s},5~{r},6~{s})-5-methoxy-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,5,7,9,13-pentamethyl-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13-pentaen-2-one (1 kDa, Ligand)
- Atp synthase subunit gamma (30 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit beta (51 kDa, Protein from Saccharomyces cerevisiae)
Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3)
Resolution: 7.6 Å
EM Method: Single-particle
Fitted PDBs: 5voz
Q-score: 0.214
Zhao J, Beyrakhova K, Liu Y, Alvarez CP, Bueler SA, Xu L, Xu C, Boniecki MT, Kanelis V, Luo ZQ, Cygler M, Rubinstein JL
PLoS Pathog (2017) 13 pp. e1006394-e1006394 [ Pubmed: 28570695 DOI: doi:10.1371/journal.ppat.1006394 ]
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit b (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-atpase:sidk complex (Complex)
- V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-atpase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c (44 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit h (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Sidk (Complex from Legionella pneumophila subsp. pneumophila ATCC 43290)
- Uncharacterized protein (65 kDa, Protein from Legionella pneumophila subsp. pneumophila ATCC 43290)
- V-type proton atpase subunit e (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase catalytic subunit a,v-type proton atpase catalytic subunit a (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit g (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit d (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit f (4 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit a, vacuolar isoform (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))