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 ]
- 5'-deoxyadenosine (251 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Human elp123 in complex with glutamine trna, desulpho-coa, 5'-deoxyadenosine and methionine (635 kDa, Complex from Homo sapiens)
- Desulfo-coenzyme a (735 Da, Ligand)
- Elongator complex protein 3 (65 kDa, Protein from Homo sapiens)
- Elongator complex protein 1 (150 kDa, Protein from Homo sapiens)
- Elongator complex protein 2 (92 kDa, Protein from Homo sapiens)
- Methionine (149 Da, Ligand)
- Trna gln (24 kDa, RNA 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)
Cryo-EM structure of yeast Elongator complex
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 8asv
Q-score: 0.372
Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Koscielniak A, Krutyholowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Glabik A, Biela A, Dobosz D, Lin TY, Abbassi NE, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S
Nucleic Acids Res (2023) 51 pp. 2011-2032 [ DOI: doi:10.1093/nar/gkac1232 Pubmed: 36617428 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Elongator complex protein 1 (153 kDa, Protein from Saccharomyces cerevisiae)
- Elongator complex protein 4 (51 kDa, Protein from Saccharomyces cerevisiae)
- Elongator complex protein 6 (30 kDa, Protein from Saccharomyces cerevisiae)
- Elongator complex protein 5 (35 kDa, Protein from Saccharomyces cerevisiae)
- Elongator complex protein 3 (63 kDa, Protein from Saccharomyces cerevisiae)
- Yeast elongator complex (845 kDa, Complex from Saccharomyces cerevisiae)
- Elongator complex protein 2 (89 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7u5c
Q-score: 0.33
Cai SW, Zinder JC, Svetlov V, Bush MW, Nudler E, Walz T, de Lange T
Nat Struct Mol Biol (2022) 29 pp. 813-819 [ Pubmed: 35578024 DOI: doi:10.1038/s41594-022-00766-y ]
- Dna primase small subunit (49 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase alpha catalytic subunit (129 kDa, Protein from Homo sapiens)
- Cst complex subunit stn1 (42 kDa, Protein from Homo sapiens)
- Cst complex subunit ten1 (13 kDa, Protein from Homo sapiens)
- Dna polymerase alpha subunit b (66 kDa, Protein from Homo sapiens)
- Human cst bound to dna polymerase alpha(pola1 delta n)-primase in a recruitment state (500 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Cst complex subunit ctc1 (135 kDa, Protein from Homo sapiens)
- Dna primase large subunit (59 kDa, Protein from Homo sapiens)
- Canonical telomeric dna sequence (5 kDa, DNA from Homo sapiens)
RNA polymerase II pre-initiation complex (PIC2)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7ml1
Q-score: 0.291
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ Pubmed: 35051353 DOI: doi:10.1016/j.molcel.2021.12.020 ]
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Baker's yeast)
- Template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Rna polymerase ii pre-initiation complex (pic2) (Complex from Saccharomyces cerevisiae)
- Non-template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Baker's yeast)
- Tfb1 (58 kDa, Protein from Baker's yeast)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Baker's yeast)
- Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Baker's yeast)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Baker's yeast)
- Transcription initiation factor iib (38 kDa, Protein from Baker's yeast)
- Dna+tfiia+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Baker's yeast)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Baker's yeast)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Baker's yeast)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Baker's yeast)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Baker's yeast)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Baker's yeast)
- Tata-box-binding protein (27 kDa, Protein from Baker's yeast)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Baker's yeast)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Tfiih (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Baker's yeast)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Baker's yeast)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Baker's yeast)
CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 7opl
Q-score: 0.275
Kilkenny ML, Veale CE, Guppy A, Hardwick SW, Chirgadze DY, Rzechorzek NJ, Maman JD, Pellegrini L
Protein Sci (2022) 31 pp. 333-344 [ Pubmed: 34719824 DOI: doi:10.1002/pro.4220 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Complex of dna polymerase alpha - primase bound to sars cov-2 nsp1 (310 kDa, Complex from Homo sapiens)
- Non-structural protein 1 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Dna primase large subunit (58 kDa, Protein from Homo sapiens)
- Dna primase small subunit (52 kDa, Protein from Homo sapiens)
- Dna polymerase alpha subunit b (49 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna polymerase alpha catalytic subunit (133 kDa, Protein from Homo sapiens)
Human polymerase delta holoenzyme Conformer 1
Resolution: 4.27 Å
EM Method: Single-particle
Fitted PDBs: 6s1m
Q-score: 0.239
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 pp. 1109-1109 [ Pubmed: 32111820 DOI: doi:10.1038/s41467-020-14898-6 ]
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Dna primer (7 kDa, DNA from synthetic construct)
- Pold holoenzyme (Complex)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase delta subunit 3 (52 kDa, Protein from Homo sapiens)
- Dna polymerase delta subunit 2 (51 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna polymerase delta subunit 4 (16 kDa, Protein from Homo sapiens)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Human polymerase delta (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna template (11 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (Complex from Homo sapiens)
- Dna polymerase delta catalytic subunit (123 kDa, Protein from Homo sapiens)
Human polymerase delta holoenzyme Conformer 2
Resolution: 4.86 Å
EM Method: Single-particle
Fitted PDBs: 6s1n
Q-score: 0.162
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 pp. 1109-1109 [ Pubmed: 32111820 DOI: doi:10.1038/s41467-020-14898-6 ]
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Dna primer (7 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- Pold holoenzyme (Complex)
- Dna polymerase delta subunit 3 (52 kDa, Protein from Homo sapiens)
- Dna polymerase delta subunit 2 (51 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna polymerase delta subunit 4 (16 kDa, Protein from Homo sapiens)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Human polymerase delta (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna template (11 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (Complex from Homo sapiens)
- Dna polymerase delta catalytic subunit (123 kDa, Protein from Homo sapiens)