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Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ip0
Q-score: 0.326
Lu M, Yu C, Zhang Y, Ju W, Ye Z, Hua C, Mao J, Hu C, Yang Z, Xiao Y
Nat Commun (2024) 15 pp. 4126-4126 [ Pubmed: 38750051 DOI: doi:10.1038/s41467-024-48598-2 ]
- Dna (5'-d(p*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (3 kDa, DNA from synthetic construct)
- Dna (41-mer) (12 kDa, DNA from synthetic construct)
- Cryo-em structure of synechocystis sp. pcc6714 cascade bound to a pam-containing dsdna target presented as full r-loop formed state at 3.6 angstrom resolution (Complex from Synechocystis sp. PCC 6714)
- Rna (44-mer) (13 kDa, RNA from synthetic construct)
- Dna (5'-d(p*tp*cp*cp*ap*tp*gp*tp*tp*tp*ap*tp*cp*ap*cp*c)-3') (4 kDa, DNA from synthetic construct)
- Type i-myxan crispr-associated protein cmx8 (63 kDa, Protein from Synechocystis sp. PCC 6714)
- Crispr associated protein cas11b (14 kDa, Protein from Synechocystis sp. PCC 6714)
- Fruiting body developmental protein r-like protein (33 kDa, Protein from Synechocystis sp. PCC 6714)
- Type i-myxan crispr-associated protein cas5/cmx5/devs (26 kDa, Protein from Synechocystis sp. PCC 6714)
Cryo-EM structure of the bacterial replication origin opening basal unwinding system
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8btg
Q-score: 0.298
Pelliciari S, Bodet-Lefevre S, Fenyk S, Stevens D, Winterhalter C, Schramm FD, Pintar S, Burnham DR, Merces G, Richardson TT, Tashiro Y, Hubbard J, Yardimci H, Ilangovan A, Murray H
Nat Commun (2023) 14 pp. 8339- [ DOI: doi:10.1093/nar/gkac1060 Pubmed: 38097584 ]
- Basal unwinding complex (Complex from Bacillus subtilis)
- Chromosomal replication initiator protein dnaa (50 kDa, Protein from Bacillus subtilis)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna (5'-d(p*ap*cp*tp*tp*ap*tp*cp*cp*ap*cp*ap*ap*ap*tp*cp*cp*ap*cp*ap*gp*gp*cp*cp*c)-3') (7 kDa, DNA from DNA molecule)
- Dna (41-mer) (12 kDa, DNA from DNA molecule)
Structural insights into human co-transcriptional capping - structure 3
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8p4c
Q-score: 0.297
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
Structural insights into human co-transcriptional capping - structure 4
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8p4d
Q-score: 0.348
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (6 kDa, RNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
Thermus thermophilus Rho-engaged RNAP elongation complex
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8hsr
Q-score: 0.317
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093-eade7093 [ DOI: doi:10.1126/sciadv.ade7093 Pubmed: 36753546 ]
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Beryllium trifluoride ion (66 Da, Ligand)
- Rho-engaged rna polymerase elongation complex (Complex from Thermus thermophilus HB8)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transcription termination factor rho (47 kDa, Protein from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Dna (31-mer) (54 kDa, DNA from synthetic construct)
- Dna (41-mer) (57 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Rna (29-mer) (39 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
Cryo-EM map of semi-attached mutant OCCM-DNA complex (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6wgc
Q-score: 0.301
Yuan Z, Schneider S, Dodd T, Riera A, Bai L, Yan C, Magdalou I, Ivanov I, Stillman B, Li H, Speck C
PNAS (2020) 117 pp. 17747-17756 [ DOI: doi:10.1073/pnas.2006231117 Pubmed: 32669428 ]
- Origin recognition complex subunit 5 (55 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Origin recognition complex subunit 1 (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Dna (41-mer) (12 kDa, DNA from Saccharomyces cerevisiae)
- Origin recognition complex subunit 3 (72 kDa, Protein from Saccharomyces cerevisiae)
- Orc-cdc6-mcm3-mcm7-dsdna (Complex from Saccharomyces cerevisiae)
- Origin recognition complex subunit 2 (71 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 6 (50 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna (41-mer) (12 kDa, DNA from Saccharomyces cerevisiae)
- Cell division control protein 6 (58 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 4 (60 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM map of pre-insertion mutant OCCM-DNA complex (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation)
Resolution: 8.1 Å
EM Method: Single-particle
Fitted PDBs: 6wgg
Q-score: 0.104
Yuan Z, Schneider S, Dodd T, Riera A, Bai L, Yan C, Magdalou I, Ivanov I, Stillman B, Li H, Speck C
PNAS (2020) 117 pp. 17747-17756 [ DOI: doi:10.1073/pnas.2006231117 Pubmed: 32669428 ]
- Origin recognition complex subunit 5 (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 1 (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (41-mer) (12 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 3 (72 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 2 (71 kDa, Protein from Saccharomyces cerevisiae)
- Cell division cycle protein cdt1 (68 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 6 (50 kDa, Protein from Saccharomyces cerevisiae)
- Dna (41-mer) (12 kDa, DNA from Saccharomyces cerevisiae)
- Orc-cdc6-mcm2-7-dsdna (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 6 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 4 (60 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 6j50
Q-score: 0.195
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ DOI: doi:10.1126/science.aav8912 Pubmed: 30733384 ]
- Dna (41-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna (5'-r(p*gp*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*u)-3') (5 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (41-mer) (12 kDa, DNA from synthetic construct)
- Protein that forms a complex with spt4p (101 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii elongation complex bound with spt4/5 and foreign dna, stalled at shl(-1) of the nucleosome (tilted conformation) (Complex from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 6cg0
Q-score: 0.452
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W
Mol Cell (2018) 70 pp. 358-370.e4 [ DOI: doi:10.1016/j.molcel.2018.03.008 Pubmed: 29628308 ]
- Dna (46-mer) (14 kDa, DNA from Escherichia coli K-12)
- Dna (30-mer) (9 kDa, DNA from Escherichia coli K-12)
- V(d)j recombination-activating protein 1 (88 kDa, Protein from Mus musculus)
- Rag1/2 in complex with nicked dnas (Complex from Mus musculus)
- Dna (5'-d(*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (4 kDa, DNA from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Dna (60-mer) (18 kDa, DNA from Escherichia coli K-12)
- High mobility group protein b1 (14 kDa, Protein from Homo sapiens)
- Dna (41-mer) (12 kDa, DNA from Escherichia coli K-12)
- Dna (5'-d(p*cp*tp*gp*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (5 kDa, DNA from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- V(d)j recombination-activating protein 2 (58 kDa, Protein from Mus musculus)
Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6cij
Q-score: 0.409
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W
Mol Cell (2018) 70 pp. 358-370.e4 [ DOI: doi:10.1016/j.molcel.2018.03.008 Pubmed: 29628308 ]
- Dna (60-mer) (18 kDa, DNA from Homo sapiens)
- Rag1/2 in complex with nicked dnas (Complex from Mus musculus)
- High mobility group protein b1 (18 kDa, Protein from Homo sapiens)
- Dna (5'-d(*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (4 kDa, DNA from Homo sapiens)
- Dna (30-mer) (9 kDa, DNA from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- V(d)j recombination-activating protein 1 (88 kDa, Protein from Mus musculus)
- Dna (41-mer) (12 kDa, DNA from Homo sapiens)
- Dna (5'-d(p*cp*tp*gp*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (6 kDa, DNA from Homo sapiens)
- Dna (46-mer) (14 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- V(d)j recombination-activating protein 2 (58 kDa, Protein from Mus musculus)