human co-transcriptional RNA capping enzyme RNGTT
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8w8e
Q-score: 0.265
Nat Commun (2024) 15 pp. 4622-4622 [ DOI: doi:10.1038/s41467-024-48963-1 Pubmed: 38816438 ]
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Negative elongation factor, transcription elongation factor, mrna-capping enzyme (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Human co-transcriptional rna capping enzyme rngtt (Complex)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna (5'-d(*(gtp))-r(p*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna (45-mer) (14 kDa, DNA from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna,rna (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polimerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna (36-mer) (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
human co-transcriptional RNA capping enzyme RNGTT-CMTR1
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8w8f
Q-score: 0.228
Nat Commun (2024) 15 pp. 4622-4622 [ DOI: doi:10.1038/s41467-024-48963-1 Pubmed: 38816438 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription elongation factor, m-rna capping enzyme, cmtr1 (Complex from Homo sapiens)
- Dna-rna (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Rna (5'-r(p*gp*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna (45-mer) (14 kDa, DNA from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Human co-transcriptional rna capping enzyme rngtt-cmtr1 (Complex)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
- Dna (36-mer) (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8atv
Q-score: 0.501
Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K
Nature (2023) 622 pp. 872-879 [ DOI: doi:10.1038/s41586-023-06643-y Pubmed: 37821701 ]
- Mitochondrial transcription factor 1 (Complex from Saccharomyces cerevisiae S288C)
- Dna (36-mer) (Complex from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase, mitochondrial (143 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpapapa) (1 kDa, RNA from Saccharomyces cerevisiae S288C)
- Dna (36-mer) (10 kDa, DNA from Saccharomyces cerevisiae S288C)
- Dna (36-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Mitochondrial transcription factor 1 (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Rna (pppgpgpapapa) (Complex from Saccharomyces cerevisiae S288C)
- Yeast mitochondrial rna polymerase transcription initiation complex with 5-mer rna, pppgpgpapapa (ic5) (143 kDa, Complex)
- Dna-directed rna polymerase, mitochondrial (Complex from Saccharomyces cerevisiae S288C)
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 8atw
Q-score: 0.447
Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K
Nature (2023) 622 pp. 872-879 [ DOI: doi:10.1038/s41586-023-06643-y Pubmed: 37821701 ]
- Mitochondria transcription factor 1 (Complex from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpapapapu) (1 kDa, RNA from Saccharomyces cerevisiae S288C)
- Template dna (36-mer) (10 kDa, DNA from Saccharomyces cerevisiae S288C)
- Dna (36-mer) (Complex from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase, mitochondrial (143 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpapapapu) (Complex from Saccharomyces cerevisiae S288C)
- Non-template dna (36-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Mitochondrial transcription factor 1 (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast mitochondrial rna polymerase transcription initiation complex with 6-mer rna, pppgpgpapapapu (ic6) (143 kDa, Complex)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polymerase, mitochondrial (Complex from Saccharomyces cerevisiae S288C)
Cryo-EM structure of Cas1:Cas2-DEDDh:half-site integration complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8fyb
Q-score: 0.453
Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA
Nature (2023) 618 pp. 855-861 [ Pubmed: 37316664 DOI: doi:10.1038/s41586-023-06178-2 ]
- Cas1 (35 kDa, Protein from Megasphaera)
- Dna (31-mer) (10 kDa, DNA from Megasphaera)
- Cas2-deddh (32 kDa, Protein from Megasphaera)
- Dna (52-mer) (19 kDa, DNA from Megasphaera)
- Dna (36-mer) (23 kDa, DNA from Megasphaera)
- Dna (17-mer) (13 kDa, DNA from Megasphaera)
- Cas1:cas2-deddh:half-site integration complex (272 kDa, Complex from Megasphaera)
Mot1:TBP:DNA - pre-hydrolysis state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7zke
Q-score: 0.377
Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP
Nat Struct Mol Biol (2023) 30 pp. 640-649 [ DOI: doi:10.1038/s41594-023-00966-0 Pubmed: 37106137 ]
- Helicase-like protein (211 kDa, Protein from Chaetomium thermophilum)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)
- Mot1:tbp:dna complex in pre-hydrolysis conformation (Complex from Chaetomium thermophilum)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Putative tata-box binding protein (29 kDa, Protein from Chaetomium thermophilum)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)
Cryo-EM structure of the Cas12m2-crRNA-target DNA ternary complex intermediate state
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 8hhm
Q-score: 0.454
Omura SN, Nakagawa R, Sudfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O
Nat Struct Mol Biol (2023) 30 pp. 1172-1182 [ DOI: doi:10.1038/s41594-023-01042-3 Pubmed: 37460897 ]
- Cas12m2-crrna-target dna (Complex from Mycolicibacterium mucogenicum)
- Dna (36-mer) (11 kDa, DNA from Mycolicibacterium mucogenicum)
- Crrna (Complex)
- Cas12m2 (Complex)
- Rna (56-mer) (18 kDa, RNA from Mycolicibacterium mucogenicum)
- Dna (36-mer) (10 kDa, DNA from Mycolicibacterium mucogenicum)
- Crrna-target dna (Complex)
- Magnesium ion (24 Da, Ligand)
- Target dna (Complex)
- Cas12m2 (66 kDa, Protein from Mycolicibacterium mucogenicum)
- Zinc ion (65 Da, Ligand)
Mot1(1-1836):TBP:DNA - post-hydrolysis complex dimer
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7zb5
Q-score: 0.456
Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP
Nat Struct Mol Biol (2023) 30 pp. 640-649 [ DOI: doi:10.1038/s41594-023-00966-0 Pubmed: 37106137 ]
- Mot1(1-1836):tbp:dna complex dimer (Complex from Chaetomium thermophilum)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)
- Helicase-like protein (206 kDa, Protein from Chaetomium thermophilum)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)
- Putative tata-box binding protein (29 kDa, Protein from Chaetomium thermophilum)
Mot1E1434Q:TBP:DNA - substrate recognition state
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7z7n
Q-score: 0.242
Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP
Nat Struct Mol Biol (2023) 30 pp. 640-649 [ DOI: doi:10.1038/s41594-023-00966-0 Pubmed: 37106137 ]
- Helicase-like protein (211 kDa, Protein from Chaetomium thermophilum)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)
- Mot1e1434q:tbp:dna complex (Complex from Chaetomium thermophilum)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)
- Putative tata-box binding protein (29 kDa, Protein from Chaetomium thermophilum)
Mot1:TBP:DNA - post hydrolysis state
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7z8s
Q-score: 0.403
Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP
Nat Struct Mol Biol (2023) 30 pp. 640-649 [ DOI: doi:10.1038/s41594-023-00966-0 Pubmed: 37106137 ]
- Helicase-like protein (211 kDa, Protein from Chaetomium thermophilum)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)
- Mot1:tbp:dna post hydrolysis complex (Complex from Chaetomium thermophilum)
- Putative tata-box binding protein (29 kDa, Protein from Chaetomium thermophilum)
- Dna (36-mer) (11 kDa, DNA from DNA molecule)