30S mRNA delivery complex TEC resolved (TEC only)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 9gur
Q-score: 0.301
Webster MW, Chauvier A, Rahil H, Graziadei A, Charles K, Miropolskaya N, Takacs M, Saint-Andre C, Rappsilber J, Walter NG, Weixlbaumer A
Science (2024) 386 pp. eado8476-eado8476 [ DOI: doi:10.1126/science.ado8476 Pubmed: 39607923 ]
- Template dna strand (9 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Non-template dna strand (9 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (25 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (25 kDa, Protein from Escherichia coli K-12)
- Mrna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (150 kDa, Protein from Escherichia coli K-12)
- Transcription elongation complex (Complex from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Transcription termination/antitermination protein nusg (13 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Template strand dna (ts31mt) (10 kDa, DNA from synthetic construct)
- Non-template strand dna (nt27mt) (10 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8u8v
Q-score: 0.405
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Substrate atp bound to insertion site (is) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Template strand dna (ts31mt) (10 kDa, DNA from synthetic construct)
- Non-template strand dna (nt27mt) (10 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Non-cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Non-template strand dna (nt27mt_+1t) (10 kDa, DNA from synthetic construct)
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Template strand dna (ts31mt_+1a) (10 kDa, DNA from synthetic construct)
NTP-bound Pol IV transcription elongation complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8xmb
Q-score: 0.43
Fang C, Huang K, Wu X, Zhang H, Gu Z, Wang J, Zhang Y
Sci Adv (2024) 10 pp. eadq3087-eadq3087 [ DOI: doi:10.1126/sciadv.adq3087 Pubmed: 39178250 ]
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from Arabidopsis thaliana)
- Rna (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase iv subunit 7 (19 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
- Template_dna (9 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Ntp-bound pol iv transcription elongation complex (650 kDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Arabidopsis thaliana)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polymerase iv subunit 1 (168 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Rna-dependent rna polymerase 2 (129 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 4 (22 kDa, Protein from Arabidopsis thaliana)
- Nontemplate_dna (6 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
Post-translocated Pol IV transcription elongation complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8xmc
Q-score: 0.417
Fang C, Huang K, Wu X, Zhang H, Gu Z, Wang J, Zhang Y
Sci Adv (2024) 10 pp. eadq3087-eadq3087 [ DOI: doi:10.1126/sciadv.adq3087 Pubmed: 39178250 ]
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from Arabidopsis thaliana)
- Post-translocated pol iv transcription elongation complex (650 kDa, Complex from Arabidopsis thaliana)
- Rna (4 kDa, RNA from synthetic construct)
- Template dna (9 kDa, DNA from synthetic construct)
- Non-template dna (6 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase iv subunit 7 (19 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase iv subunit 1 (168 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Rna-dependent rna polymerase 2 (129 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 4 (22 kDa, Protein from Arabidopsis thaliana)
- Zinc ion (65 Da, Ligand)
Pre-translocated Pol IV transcription elongation complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8xmd
Q-score: 0.383
Fang C, Huang K, Wu X, Zhang H, Gu Z, Wang J, Zhang Y
Sci Adv (2024) 10 pp. eadq3087-eadq3087 [ DOI: doi:10.1126/sciadv.adq3087 Pubmed: 39178250 ]
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from Arabidopsis thaliana)
- Template_dna (10 kDa, DNA from synthetic construct)
- Pre-translocated pol iv transcription elongation complex (650 kDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerase iv subunit 7 (19 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase iv subunit 1 (168 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Rna-dependent rna polymerase 2 (129 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 4 (22 kDa, Protein from Arabidopsis thaliana)
- Nontemplate_dna (6 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (5 kDa, RNA from synthetic construct)
Backtracked Pol IV transcription elongation complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8xme
Q-score: 0.377
Fang C, Huang K, Wu X, Zhang H, Gu Z, Wang J, Zhang Y
Sci Adv (2024) 10 pp. eadq3087-eadq3087 [ DOI: doi:10.1126/sciadv.adq3087 Pubmed: 39178250 ]
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from Arabidopsis thaliana)
- Template_dna (12 kDa, DNA from synthetic construct)
- Backtracked pol iv transcription elongation complex (650 kDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerase iv subunit 7 (19 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase iv subunit 1 (168 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Rna-dependent rna polymerase 2 (129 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 4 (22 kDa, Protein from Arabidopsis thaliana)
- Zinc ion (65 Da, Ligand)
- Nontemplate_dna (12 kDa, DNA from synthetic construct)
- Rna (5 kDa, RNA from synthetic construct)
Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8oki
Q-score: 0.48
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna template strand (8 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Transcription elongation complex with spt4/5 (Complex)
- Dna non-template strand (7 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Spt4/5 (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
E. coli RNA polymerase paused at ops site
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8pdy
Q-score: 0.409
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Transcription elongation complex paused at ops site, assembled on fully complementary nucleic acid scaffold (399 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Rna (5'-r(p*up*gp*gp*cp*gp*gp*up*ap*gp*cp*gp*u)-3') (5 kDa, RNA from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Non-template dna (35-mer) (12 kDa, DNA from Escherichia coli)