Complete DNA elongation subcomplex of Xenopus laevis DNA polymerase alpha-primase
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8g9o
Q-score: 0.275
Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF
Nat Struct Mol Biol (2024) 31 pp. 777-790 [ DOI: doi:10.1038/s41594-024-01227-4 Pubmed: 38491139 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Primase (Complex from Xenopus laevis)
- Dna polymerase alpha catalytic subunit (129 kDa, Protein from Xenopus laevis)
- Dna primase large subunit (59 kDa, Protein from Xenopus laevis)
- Polymerase alpha (Complex from Xenopus laevis)
- Dna template (15 kDa, DNA from synthetic construct)
- Rna-dna primer (6 kDa, Macromolecule from synthetic construct)
- 2'-deoxyguanosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna elongation substrate (20 kDa, Complex from synthetic construct)
- Polymerase alpha-primase with a dna elongation substrate (110 kDa, Complex)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6u8y
Q-score: 0.414
Yu H, Haja DK, Schut GJ, Wu CH, Meng X, Zhao G, Li H, Adams MWW
Nat Commun (2020) 11 pp. 5953-5953 [ DOI: doi:10.1038/s41467-020-19697-7 Pubmed: 33230146 ]
- Duf4040 domain-containing protein (10 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit n (53 kDa, Protein from Pyrococcus furiosus COM1)
- Iron/sulfur cluster (351 Da, Ligand)
- Monovalent cation/h+ antiporter subunit c (12 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit g (13 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit c (20 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit (33 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit b (25 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit i (24 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit e (19 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit f (9 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit b (22 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit m (67 kDa, Protein from Pyrococcus furiosus COM1)
- Respiratory membrane complex (Complex from Pyrococcus furiosus)
- Nadh dehydrogenase subunit d (44 kDa, Protein from Pyrococcus furiosus COM1)
Cryo-EM structure of respiratory complex I from Yarrowia lipolytica
Resolution: 4.32 Å
EM Method: Single-particle
Fitted PDBs: 6gcs
Q-score: 0.371
Parey K, Brandt U, Xie H, Mills DJ, Siegmund K, Vonck J, Kuehlbrandt W, Zickermann V
eLife (2018) 7 [ DOI: doi:10.7554/eLife.39213 Pubmed: 30277212 ]
- Flavin mononucleotide (456 Da, Ligand)
- Nunm subunit (7 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Acpm1 subunit (12 kDa, Protein from Yarrowia lipolytica)
- Nuum subunit (3 kDa, Protein from Yarrowia lipolytica)
- Mitochondrial nadh:ubiquinone oxidoreductase (963 MDa, Complex from Yarrowia lipolytica)
- 49-kda protein (nucm) (52 kDa, Protein from Yarrowia lipolytica)
- Ni2m subunit (12 kDa, Protein from Yarrowia lipolytica)
- Nuxm subunit (18 kDa, Protein from Yarrowia lipolytica)
- 1,2-diacyl-sn-glycero-3-phosphoethanolamine (748 Da, Ligand)
- Nebm subunit (5 kDa, Protein from Yarrowia lipolytica)
- Acpm2 subunit (14 kDa, Protein from Yarrowia lipolytica)
- 24-kda subunit (nuhm) (27 kDa, Protein from Yarrowia lipolytica)
- Nb5m subunit (10 kDa, Protein from Yarrowia lipolytica)
- Unknown subunit (4 kDa, Protein from Yarrowia lipolytica)
- Nipm subunit (10 kDa, Protein from Yarrowia lipolytica)
- Nb8m subunit (11 kDa, Protein from Yarrowia lipolytica)
- Nesm subunit (13 kDa, Protein from Yarrowia lipolytica)
- N7bm subunit (16 kDa, Protein from Yarrowia lipolytica)
- Nufm subunit (16 kDa, Protein from Yarrowia lipolytica)
- Niam subunit (8 kDa, Protein from Yarrowia lipolytica)
- Numm subunit (15 kDa, Protein from Yarrowia lipolytica)
- Nidm subunit (11 kDa, Protein from Yarrowia lipolytica)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nupm subunit (19 kDa, Protein from Yarrowia lipolytica)
- 30-kda protein (nugm) (32 kDa, Protein from Yarrowia lipolytica)
- Nuym subunit (18 kDa, Protein from Yarrowia lipolytica)
- Nd3 subunit (nu3m) (14 kDa, Protein from Yarrowia lipolytica)
- Nujm subunit (20 kDa, Protein from Yarrowia lipolytica)
- Iron/sulfur cluster (351 Da, Ligand)
- Nimm subunit (9 kDa, Protein from Yarrowia lipolytica)
- Nd4 subunit (nu4m) (54 kDa, Protein from Yarrowia lipolytica)
- S-[2-({n-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate (568 Da, Ligand)
- Nuzm subunit (11 kDa, Protein from Yarrowia lipolytica)
- Tyky subunit (nuim) (25 kDa, Protein from Yarrowia lipolytica)
- Nd4l subunit (nulm) (9 kDa, Protein from Yarrowia lipolytica)
- Psst subunit (nukm) (23 kDa, Protein from Yarrowia lipolytica)
- Ni9m subunit (7 kDa, Protein from Yarrowia lipolytica)
- Nd2 subunit (nu2m) (53 kDa, Protein from Yarrowia lipolytica)
- Zinc ion (65 Da, Ligand)
- Nuem subunit (42 kDa, Protein from Yarrowia lipolytica)
- Nb4m subunit (14 kDa, Protein from Yarrowia lipolytica)
- 51-kda protein (nubm) (53 kDa, Protein from Yarrowia lipolytica)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Nb6m subunit (14 kDa, Protein from Yarrowia lipolytica)
- Nd1 subunit (nu1m) (38 kDa, Protein from Yarrowia lipolytica)
- Nd5 subunit (nu5m) (73 kDa, Protein from Yarrowia lipolytica)
- Nd6 subunit (nu6m) (20 kDa, Protein from Yarrowia lipolytica)
- Ni8m subunit (9 kDa, Protein from Yarrowia lipolytica)
- Nb2m subunit (6 kDa, Protein from Yarrowia lipolytica)
- 75-kda protein (nuam) (79 kDa, Protein from Yarrowia lipolytica)
Cryo-EM structure of a respiratory complex I mutant lacking NDUFS4
Resolution: 4.04 Å
EM Method: Single-particle
Fitted PDBs: 6rfs
Q-score: 0.342
Parey K, Haapanen O, Sharma V, Kofeler H, Zullig T, Prinz S, Siegmund K, Wittig I, Mills DJ, Vonck J, Kuhlbrandt W, Zickermann V
Sci Adv (2019) 5 pp. eaax9484-eaax9484 [ Pubmed: 31844670 DOI: doi:10.1126/sciadv.aax9484 ]
- Subunit nuam of nadh:ubiquinone oxidoreductase (complex i) (79 kDa, Protein from Candida lipolytica)
- Subunit nufm of nadh:ubiquinone oxidoreductase (complex i) (16 kDa, Protein from Yarrowia lipolytica)
- Subunit nu2m of nadh:ubiquinone oxidoreductase (complex i) (53 kDa, Protein from Yarrowia lipolytica)
- Subunit nu5m of nadh:ubiquinone oxidoreductase (complex i) (73 kDa, Protein from Yarrowia lipolytica)
- Acyl carrier protein acpm1 of nadh:ubiquinone oxidoreductase (complex i) (12 kDa, Protein from Candida lipolytica)
- Subunit nukm of nadh:ubiquinone oxidoreductase (complex i) (23 kDa, Protein from Candida lipolytica)
- Subunit nupm of nadh:ubiquinone oxidoreductase (complex i) (19 kDa, Protein from Yarrowia lipolytica)
- Subunit nubm of nadh:ubiquinone oxidoreductase (complex i) (53 kDa, Protein from Candida lipolytica)
- Subunit nimm of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Candida lipolytica)
- Subunit ni2m of nadh:ubiquinone oxidoreductase (complex i) (12 kDa, Protein from Candida lipolytica)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Subunit ni9m of nadh:ubiquinone oxidoreductase (complex i) (8 kDa, Protein from Yarrowia lipolytica)
- Subunit nuvm of nadh:ubiquinone oxidoreductase (complex i) (7 kDa, Protein from Yarrowia lipolytica)
- Subunit nb4m of protein nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Candida lipolytica)
- Acyl carrier protein acpm2 of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Candida lipolytica)
- Subunit nucm of nadh:ubiquinone oxidoreductase (complex i) (52 kDa, Protein from Candida lipolytica)
- Flavin mononucleotide (456 Da, Ligand)
- Subunit nidm of nadh:ubiquinone oxidoreductase (complex i) (11 kDa, Protein from Candida lipolytica)
- Subunit nb2m of nadh:ubiquinone oxidoreductase (complex i) (6 kDa, Protein from Yarrowia lipolytica)
- Subunit nujm of nadh:ubiquinone oxidoreductase (complex i) (20 kDa, Protein from Yarrowia lipolytica)
- Subunit nu4m of nadh:ubiquinone oxidoreductase (complex i) (54 kDa, Protein from Yarrowia lipolytica)
- Subunit ni8m of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Candida lipolytica)
- Subunit n7bm of nadh:ubiquinone oxidoreductase (complex i) (16 kDa, Protein from Yarrowia lipolytica)
- Subunit nuxm of nadh:ubiquinone oxidoreductase (complex i) (18 kDa, Protein from Candida lipolytica)
- Subunit nu1m of nadh:ubiquinone oxidoreductase (complex i) (38 kDa, Protein from Yarrowia lipolytica)
- Subunit nunm of nadh:ubiquinone oxidoreductase (complex i) (13 kDa, Protein from Yarrowia lipolytica)
- Subunit niam of nadh:ubiquinone oxidoreductase (complex i) (17 kDa, Protein from Yarrowia lipolytica)
- Subunit nebm of nadh:ubiquinone oxidoreductase (complex i) (8 kDa, Protein from Yarrowia lipolytica)
- Subunit nuhm of nadh:ubiquinone oxidoreductase (complex i) (27 kDa, Protein from Candida lipolytica)
- Subunit nb5m of nadh:ubiquinone oxidoreductase (complex i) (10 kDa, Protein from Candida lipolytica)
- Subunit numm of nadh:ubiquinone oxidoreductase (complex i) (15 kDa, Protein from Candida lipolytica)
- Mitochondrial nadh:ubiquinone oxidoreductase (1 MDa, Complex from Yarrowia lipolytica)
- S-[2-({n-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate (568 Da, Ligand)
- Subunit nuim of nadh:ubiquinone oxidoreductase (complex i) (25 kDa, Protein from Candida lipolytica)
- Subunit nb8m of nadh:ubiquinone oxidoreductase (complex i) (11 kDa, Protein from Candida lipolytica)
- Subunit nulm of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Yarrowia lipolytica)
- Zinc ion (65 Da, Ligand)
- Subunit nuzm of nadh:ubiquinone oxidoreductase (complex i) (19 kDa, Protein from Yarrowia lipolytica)
- Subunit nipm of nadh:ubiquinone oxidoreductase (complex i) (10 kDa, Protein from Candida lipolytica)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Subunit nu3m of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Yarrowia lipolytica)
- Subunit nesm of nadh:ubiquinone oxidoreductase (complex i) (28 kDa, Protein from Yarrowia lipolytica)
- Subunit nugm of nadh:ubiquinone oxidoreductase (complex i) (32 kDa, Protein from Candida lipolytica)
- Iron/sulfur cluster (351 Da, Ligand)
- Subunit nuem of nadh:ubiquinone oxidoreductase (complex i) (42 kDa, Protein from Yarrowia lipolytica)
- Subunit nu6m of nadh:ubiquinone oxidoreductase (complex i) (20 kDa, Protein from Yarrowia lipolytica)
- Subunit nuum of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Yarrowia lipolytica)
- Subunit nb6m of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Candida lipolytica)
STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 5oqj
Q-score: 0.249
Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P
Nature (2017) 551 pp. 204-209 [ DOI: doi:10.1038/nature24282 Pubmed: 29088706 ]
- Template dna (32 kDa, DNA from synthetic construct)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nucleic acid (Complex from synthetic construct)
- Nontemplate dna (32 kDa, DNA from synthetic construct)
- Transcription factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Suppressor of stem-loop protein 1 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 2 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 1 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iie subunit alpha (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Polymerase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (3 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad25 (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-initiation complex (pic) (1 MDa, Complex)
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Initiation factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
The cryo-EM structure of human TFIIH
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 5of4
Q-score: 0.308
Greber BJ, Nguyen THD, Fang J, Afonine PV, Adams PD, Nogales E
Nature (2017) 549 pp. 414-417 [ DOI: doi:10.1038/nature23903 Pubmed: 28902838 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Tfiih core complex (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Human)
- Unassigned secondary structure elements. (22 kDa, Protein from Homo sapiens)
- Tfiih (Complex from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Human)
- General transcription factor iih subunit 4,p52,general transcription factor iih subunit 4 (9 kDa, Protein from Human)
- General transcription factor iih subunit 2 (44 kDa, Protein from Human)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Human)
- Unassigned secondary structure elements (p52 region) (19 kDa, Protein from Homo sapiens)
- Tfiih cdk-activating kinase (cak) subcomplex (Complex from Homo sapiens)
- Mat1 (10 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit,xpb,tfiih basal transcription factor complex helicase xpb subunit (62 kDa, Protein from Human)
- Unassigned secondary structure elements (xpb nte region) (6 kDa, Protein from Homo sapiens)