Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 8pu0
Q-score: 0.277
Abbassi NE, Jaciuk M, Scherf D, Bohnert P, Rau A, Hammermeister A, Rawski M, Indyka P, Wazny G, Chramiec-Glabik A, Dobosz D, Skupien-Rabian B, Jankowska U, Rappsilber J, Schaffrath R, Lin TY, Glatt S
Nat Commun (2024) 15 pp. 4094-4094 [ DOI: doi:10.1038/s41467-024-48251-y Pubmed: 38750017 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Trna gln (24 kDa, RNA from Homo sapiens)
- Elongator complex protein 2 (92 kDa, Protein from Homo sapiens)
- Elongator complex protein 1 (150 kDa, Protein from Homo sapiens)
- 5'-deoxyadenosine (251 Da, Ligand)
- Elongator complex protein 3 (65 kDa, Protein from Homo sapiens)
- Methionine (149 Da, Ligand)
- Desulfo-coenzyme a (735 Da, Ligand)
- Human elp123 in complex with glutamine trna, desulpho-coa, 5'-deoxyadenosine and methionine (635 kDa, Complex from Homo sapiens)
Cryo-EM structure of Tetrahymena thermophila respiratory Megacomplex MC (IV2+I+III2+II)2
Resolution: 4.18 Å
EM Method: Single-particle
Fitted PDBs: 8gzu
Q-score: 0.253
Han F, Hu Y, Wu M, He Z, Tian H, Zhou L
Nat Commun (2023) 14 pp. 2542-2542 [ DOI: doi:10.1038/s41467-023-38158-5 Pubmed: 37248254 ]
- M16 family peptidase, putative (53 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (28 kDa, Protein from Tetrahymena thermophila SB210)
- Acyl carrier protein (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (9 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (41 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf75 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (8 kDa, Protein from Tetrahymena thermophila SB210)
- Structural protein (27 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 7 (51 kDa, Protein from Tetrahymena thermophila SB210)
- Cx9c domain-containing protein (28 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (7 kDa, Protein from Tetrahymena thermophila SB210)
- Sdhtt11 (5 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub10 (22 kDa, Protein from Tetrahymena thermophila SB210)
- Cox assembly mitochondrial protein (17 kDa, Protein from Tetrahymena thermophila SB210)
- Phage protein (14 kDa, Protein from Tetrahymena thermophila SB210)
- 2-oxoglutarate/malate carrier protein (36 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome b-c1 complex subunit 8 (7 kDa, Protein from Tetrahymena thermophila SB210)
- Gamma-carbonic anhydrase (28 kDa, Protein from Tetrahymena thermophila SB210)
- Zf-tim10_ddp domain-containing protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Ndutt17 (14 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub2 (14 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (7 kDa, Protein from Tetrahymena thermophila SB210)
- Chch domain-containing protein (13 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf62 (30 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (52 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt3 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (23 kDa, Protein from Tetrahymena thermophila SB210)
- Atp synthase subunit e, mitochondrial (11 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 10 (18 kDa, Protein from Tetrahymena thermophila SB210)
- Uqcrtt2 (4 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase 24 kda subunit (31 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase complex i, 21 kda subunit (17 kDa, Protein from Tetrahymena thermophila SB210)
- Transposase (8 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase chain 3 (14 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (24 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (8 kDa, Protein from Tetrahymena thermophila SB210)
- Heme-a (852 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nadh dehydrogenase subunit 1 (7 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (26 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (21 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf70 (10 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Duf4885 domain-containing protein (12 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase 75 kda subunit (80 kDa, Protein from Tetrahymena thermophila SB210)
- Annexin (8 kDa, Protein from Tetrahymena thermophila SB210)
- Trab family protein (45 kDa, Protein from Tetrahymena thermophila SB210)
- Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein qp-c (26 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit 1 (80 kDa, Protein from Tetrahymena thermophila SB210)
- Ubiquinone-10 (863 Da, Ligand)
- Transmembrane protein, putative (9 kDa, Protein from Tetrahymena thermophila SB210)
- Rieske iron-sulfur protein, ubiquinol-cytochrome c reductase iron-sulfur subunit (30 kDa, Protein from Tetrahymena thermophila SB210)
- Complex iii subunit vii (19 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila SB210)
- Apocytochrome b (50 kDa, Protein from Tetrahymena thermophila SB210)
- Iron-binding zinc finger cdgsh type protein (21 kDa, Protein from Tetrahymena thermophila SB210)
- 2 iron, 2 sulfur cluster-binding protein (19 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (16 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (16 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (18 kDa, Protein from Tetrahymena thermophila SB210)
- Abc transporter (10 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt22 (17 kDa, Protein from Tetrahymena thermophila SB210)
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (70 kDa, Protein from Tetrahymena thermophila SB210)
- Heme c (618 Da, Ligand)
- Transmembrane protein, putative (24 kDa, Protein from Tetrahymena thermophila SB210)
- Sulphotransf domain-containing protein (39 kDa, Protein from Tetrahymena thermophila SB210)
- Gamma-carbonic anhydrase (25 kDa, Protein from Tetrahymena thermophila SB210)
- Lipid-a-disaccharide synthase (59 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub8 (24 kDa, Protein from Tetrahymena thermophila SB210)
- Yflt domain-containing protein (19 kDa, Protein from Tetrahymena thermophila SB210)
- Ubiquinol-cytochrome c reductase hinge protein (10 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial (37 kDa, Protein from Tetrahymena thermophila SB210)
- Acyl carrier protein (16 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf67 (54 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf65 (43 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (18 kDa, Protein from Tetrahymena thermophila SB210)
- Flavin mononucleotide (456 Da, Ligand)
- Ph domain-containing protein (15 kDa, Protein from Tetrahymena thermophila SB210)
- Chromosome condensation regulator rcc1 repeat protein (50 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (13 kDa, Protein from Tetrahymena thermophila SB210)
- Diphthamide synthesis protein (22 kDa, Protein from Tetrahymena thermophila SB210)
- Protein phosphatase 2c, putative (53 kDa, Protein from Tetrahymena thermophila SB210)
- Sdhd (5 kDa, Protein from Tetrahymena thermophila SB210)
- Surf1-like protein (35 kDa, Protein from Tetrahymena thermophila SB210)
- Rnase iii domain-containing protein (35 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (20 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 9 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Unknown peptide (7 kDa, Protein from Tetrahymena thermophila SB210)
- Complex i-mnll (12 kDa, Protein from Tetrahymena thermophila SB210)
- Lysozyme (12 kDa, Protein from Tetrahymena thermophila SB210)
- Fe3-s4 cluster (295 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial (22 kDa, Protein from Tetrahymena thermophila SB210)
- Decapping nuclease (10 kDa, Protein from Tetrahymena thermophila SB210)
- Tim10/ddp family zinc finger protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (29 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt10 (28 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf58 (13 kDa, Protein from Tetrahymena thermophila SB210)
- Ndutt16 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (22 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (57 kDa, Protein from Tetrahymena thermophila SB210)
- Mobilization protein (23 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (14 kDa, Protein from Tetrahymena thermophila SB210)
- Tetrahymena thermophila respiratory mega-complex mc (iv2+i+iii2+ii)2 (10 MDa, Complex from Tetrahymena thermophila SB210)
- Nduph2 (22 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (12 kDa, Protein from Tetrahymena thermophila SB210)
- Succinate dehydrogenase (quinone) (36 kDa, Protein from Tetrahymena thermophila SB210)
- Gram domain protein (10 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt9 (29 kDa, Protein from Tetrahymena thermophila SB210)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Transmembrane protein (24 kDa, Protein from Tetrahymena thermophila SB210)
- Magnesium ion (24 Da, Ligand)
- Ymf57 (12 kDa, Protein from Tetrahymena thermophila SB210)
- Cullin domain-containing protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase, putative (20 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase chain 4 (58 kDa, Protein from Tetrahymena thermophila SB210)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Transposase (11 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit 2 (72 kDa, Protein from Tetrahymena thermophila SB210)
- Copper (ii) ion (63 Da, Ligand)
- Dnaj domain protein (36 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (26 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (14 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 2 (20 kDa, Protein from Tetrahymena thermophila SB210)
- Nad-dependent epimerase/dehydratase family protein (41 kDa, Protein from Tetrahymena thermophila SB210)
- Acyl-coa synthetase (amp-forming)/amp-acid ligase ii (36 kDa, Protein from Tetrahymena thermophila SB210)
- Ndua13 (21 kDa, Protein from Tetrahymena thermophila SB210)
- Zinc-finger protein (15 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub4 (17 kDa, Protein from Tetrahymena thermophila SB210)
- Nmra domain-containing protein (36 kDa, Protein from Tetrahymena thermophila SB210)
- 39s ribosomal protein l9, mitochondrial (27 kDa, Protein from Tetrahymena thermophila SB210)
- Peptidase m16 inactive domain protein (58 kDa, Protein from Tetrahymena thermophila SB210)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Zf-tim10_ddp domain-containing protein (10 kDa, Protein from Tetrahymena thermophila SB210)
- Transcription factor apfi protein, putative (39 kDa, Protein from Tetrahymena thermophila SB210)
- Ribosomal protein l51/s25/ci-b8 domain protein (12 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt28 (11 kDa, Protein from Tetrahymena thermophila SB210)
- 37s ribosomal protein s25, mitochondrial (33 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit vb protein (75 kDa, Protein from Tetrahymena thermophila SB210)
- Sdhtt3 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf68 (72 kDa, Protein from Tetrahymena thermophila SB210)
- Zinc ion (65 Da, Ligand)
- Etc complex i subunit motif protein (24 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub6 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase chain 1 (32 kDa, Protein from Tetrahymena thermophila SB210)
- Unknown peptide (1 kDa, Protein from Tetrahymena thermophila SB210)
- Oxoglutarate/malate translocator protein, putative (40 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome protein c1 (37 kDa, Protein from Tetrahymena thermophila SB210)
- Ndutt15 (27 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (35 kDa, Protein from Tetrahymena thermophila SB210)
- Thioredoxin (19 kDa, Protein from Tetrahymena thermophila SB210)
- Carrier protein (37 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 5 (88 kDa, Protein from Tetrahymena thermophila SB210)
- Ctf/nf-i domain-containing protein (116 kDa, Protein from Tetrahymena thermophila SB210)
- Surf1-like protein (47 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase 1, chain, putative (28 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein (20 kDa, Protein from Tetrahymena thermophila SB210)
Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the RNA synthesis state
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8foh
Q-score: 0.358
Yuan Z, Georgescu R, Li H, O'Donnell ME
Nat Commun (2023) 14 pp. 3697-3697 [ DOI: doi:10.1038/s41467-023-39441-1 Pubmed: 37344454 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase alpha/primase complex (Complex from Saccharomyces cerevisiae)
- Primer rna (2 kDa, RNA from synthetic construct)
- Dna primase (47 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (3 kDa, DNA from synthetic construct)
- Dna primase large subunit (62 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase (167 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase alpha subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 8foj
Q-score: 0.336
Yuan Z, Georgescu R, Li H, O'Donnell ME
Nat Commun (2023) 14 pp. 3697-3697 [ DOI: doi:10.1038/s41467-023-39441-1 Pubmed: 37344454 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase alpha/primase complex (Complex from Saccharomyces cerevisiae)
- Dna primase (47 kDa, Protein from Saccharomyces cerevisiae)
- Dna primase large subunit (62 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase (167 kDa, Protein from Saccharomyces cerevisiae)
- Primer rna (3 kDa, RNA from synthetic construct)
- Template dna (3 kDa, DNA from synthetic construct)
- Dna polymerase alpha subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
RNA polymerase III pre-initiation complex melting complex 1
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8iue
Q-score: 0.291
Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y
Cell Res (2023) 33 pp. 565-568 [ DOI: doi:10.1038/s41422-023-00819-x Pubmed: 37165065 ]
- Dna-directed rna polymerase (Complex)
- Dna-directed rna polymerase iii subunit rpc4 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc6 (35 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Rna polymerase iii pre-initiation complex melting complex 1 (1 MDa, Complex from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc2 (127 kDa, Protein from Homo sapiens)
- Dna (74-mer) (143 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc1 (155 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc7 (25 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc9 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc3 (60 kDa, Protein from Homo sapiens)
- Transcription factor tfiiib component b'' homolog (294 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription factor iiib 50 kda subunit (46 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase iii subunit rpc5 (80 kDa, Protein from Homo sapiens)
- Transcription factor (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Human gene for u 6 rna (143 kDa, DNA from Homo sapiens)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc8 (22 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from pig)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (217 kDa, Protein from pig)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iie (Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- General transcription factor iib (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from pig)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8byq
Q-score: 0.187
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
- General transcription factor iih (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from pig)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
- Zinc ion (65 Da, Ligand)
- General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from pig)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iie (Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- General transcription factor iib (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from pig)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
Initial DNA-lesion (Cy5) binding by XPC and TFIIH
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8ebs
Q-score: 0.274
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex (580 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Dna (cy5) (16 kDa, DNA from synthetic construct)
- Dna (16 kDa, DNA from synthetic construct)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
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)
Electron bifurcating hydrogenase - HydABC from A. woodii
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 7q4v
Q-score: 0.211
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ Pubmed: 36811855 DOI: doi:10.1021/jacs.2c11683 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Homodimer complex of hydabc trimer (300 MDa, Complex from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hydb (64 kDa, Protein from Acetobacterium woodii DSM 1030)
- Flavin mononucleotide (456 Da, Ligand)
- Zinc ion (65 Da, Ligand)