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SpCas9-MMLV RT-pegRNA-target DNA complex (termination)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wus
Q-score: 0.454
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna (40-mer) (12 kDa, DNA from Streptococcus pyogenes)
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 8umv
Q-score: 0.533
He Q, Wang F, O'Donnell ME, Li H
PNAS (2024) 121 pp. e2319727121-e2319727121 [ Pubmed: 38669181 DOI: doi:10.1073/pnas.2319727121 ]
- Dna (20-mer) (6 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- The human clamp-clamp loader complex pcna-ctf18 (300 kDa, Complex from Homo sapiens)
- Replication factor c subunit 5 (38 kDa, Protein from Homo sapiens)
- Replication factor c subunit 3 (40 kDa, Protein from Homo sapiens)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 4 (39 kDa, Protein from Homo sapiens)
- Replication factor c subunit 2 (39 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Chromosome transmission fidelity protein 18 homolog (107 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8umw
Q-score: 0.495
He Q, Wang F, O'Donnell ME, Li H
PNAS (2024) 121 pp. e2319727121-e2319727121 [ Pubmed: 38669181 DOI: doi:10.1073/pnas.2319727121 ]
- Dna (20-mer) (6 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- The human clamp-clamp loader complex pcna-ctf18 (300 kDa, Complex from Homo sapiens)
- Replication factor c subunit 5 (38 kDa, Protein from Homo sapiens)
- Replication factor c subunit 3 (40 kDa, Protein from Homo sapiens)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 4 (39 kDa, Protein from Homo sapiens)
- Replication factor c subunit 2 (39 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Chromosome transmission fidelity protein 18 homolog (107 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 8umy
Q-score: 0.51
He Q, Wang F, O'Donnell ME, Li H
PNAS (2024) 121 pp. e2319727121-e2319727121 [ Pubmed: 38669181 DOI: doi:10.1073/pnas.2319727121 ]
- Dna (20-mer) (6 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- The human clamp-clamp loader complex pcna-ctf18 (300 kDa, Complex from Homo sapiens)
- Replication factor c subunit 5 (38 kDa, Protein from Homo sapiens)
- Replication factor c subunit 3 (40 kDa, Protein from Homo sapiens)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 4 (39 kDa, Protein from Homo sapiens)
- Replication factor c subunit 2 (39 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Chromosome transmission fidelity protein 18 homolog (107 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Cryo-EM map of the human CTF18-RFC-PCNA-DNA ternary complex with cracked and closed PCNA (state 7)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8un0
Q-score: 0.451
He Q, Wang F, O'Donnell ME, Li H
PNAS (2024) 121 pp. e2319727121-e2319727121 [ Pubmed: 38669181 DOI: doi:10.1073/pnas.2319727121 ]
- Dna (20-mer) (6 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- The human clamp-clamp loader complex pcna-ctf18 (300 kDa, Complex from Homo sapiens)
- Replication factor c subunit 5 (38 kDa, Protein from Homo sapiens)
- Replication factor c subunit 3 (40 kDa, Protein from Homo sapiens)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 4 (39 kDa, Protein from Homo sapiens)
- Replication factor c subunit 2 (39 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Chromosome transmission fidelity protein 18 homolog (107 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Structure of HamB-DNA complex, conformation 1, from the Escherichia coli Hachiman defense system
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8vxa
Q-score: 0.462
Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA
bioRxiv (2024) [ Pubmed: 38464307 DOI: doi:10.1101/2024.02.29.582594 ]
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Hamb-dna complex (155 kDa, Complex from Escherichia coli)
- Hamb (130 kDa, Protein from Escherichia coli)
Structure of HamB-DNA complex, conformation 2, from the Escherichia coli Hachiman defense system
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8vxc
Q-score: 0.408
Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA
bioRxiv (2024) [ Pubmed: 38464307 DOI: doi:10.1101/2024.02.29.582594 ]
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Hamb-dna complex (155 kDa, Complex from Escherichia coli)
- Hamb (130 kDa, Protein from Escherichia coli)
Cyanobacterial RNA polymerase elongation complex with NusG and CTP
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8urw
Q-score: 0.515
Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS
PNAS (2024) 121 pp. e2311480121-e2311480121 [ Pubmed: 38354263 DOI: doi:10.1073/pnas.2311480121 ]
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechococcus elongatus)
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechococcus elongatus)
- Rna (5'-r(p*ap*ap*ap*gp*ap*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (33 kDa, Protein from Synechococcus elongatus)
- Cyanobacterial rna polymerase elongation complex with nusg and ctp (Complex from Synechococcus elongatus)
- Transcription termination/antitermination protein nusg (23 kDa, Protein from Synechococcus elongatus)
- Zinc ion (65 Da, Ligand)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 8jh2
Q-score: 0.145
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ Pubmed: 37981206 DOI: doi:10.1016/j.jbc.2023.105477 ]
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*g)-3') (5 kDa, RNA from synthetic construct)
- Rna polymerase ii (Complex from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Rna polymerase subunit abc27 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
CryoEM structure of RuvA-RuvB-Holliday junction complex
Resolution: 7.02 Å
EM Method: Single-particle
Fitted PDBs: 7x7q
Q-score: 0.167
Zhang X, Zhou Z, Dai L, Chao Y, Liu Z, Huang M, Qu Q, Lin Z
Front Plant Sci (2023) 14 pp. 1139106-1139106 [ DOI: doi:10.3389/fpls.2023.1139106 Pubmed: 37025142 ]
- Holliday junction atp-dependent dna helicase ruva (21 kDa, Protein from Pseudomonas aeruginosa PAO1)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Ruva-ruvb (Complex from synthetic construct)
- Ruva-ruvb-holliday junction complex (Complex from Pseudomonas aeruginosa PAO1)
- Dna (26-mer) (7 kDa, DNA from synthetic construct)
- Dna (Complex)
- Dna (26-mer) (7 kDa, DNA from synthetic construct)
- Holliday junction atp-dependent dna helicase ruvb (38 kDa, Protein from Pseudomonas aeruginosa PAO1)