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The cryo-EM structure of the Nicotiana tabacum PEP-PAP
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8w9z
Q-score: 0.405
Wu XX, Mu WH, Li F, Sun SY, Cui CJ, Kim C, Zhou F, Zhang Y
Cell (2024) 187 pp. 1127-1144.e21 [ DOI: doi:10.1016/j.cell.2024.01.026 Pubmed: 38428393 ]
- Fructokinase-like 2, chloroplastic (72 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 14-like isoform x2 (58 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit beta (120 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit gamma (79 kDa, Protein from Nicotiana tabacum)
- Fe (iii) ion (55 Da, Ligand)
- Protein plastid transcriptionally active 7-like isoform x1 (19 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 10-like (80 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit beta'' (157 kDa, Protein from Nicotiana tabacum)
- Pap13(ptac18) (17 kDa, Protein from Nicotiana tabacum)
- Nicotiana tabacum pep-pap (Complex from Nicotiana tabacum)
- Superoxide dismutase (34 kDa, Protein from Nicotiana tabacum)
- Udp-n-acetylmuramoyl-l-alanyl-d-glutamate--2, 6-diaminopimelate ligase-like (85 kDa, Protein from Nicotiana tabacum)
- Fructokinase-like 1, chloroplastic (55 kDa, Protein from Nicotiana tabacum)
- Zinc ion (65 Da, Ligand)
- Pentatricopeptide repeat-containing protein at1g74850, chloroplastic-like (96 kDa, Protein from Nicotiana tabacum)
- Pap1(ptac3) (101 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (30 kDa, Protein from Nicotiana tabacum)
- Pap8(ptac6) (38 kDa, Protein from Nicotiana tabacum)
- Thioredoxin-like protein citrx1, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Protein plastid transcriptionally active 12-like (61 kDa, Protein from Nicotiana tabacum)
The cryo-EM structure of the Nicotiana tabacum PEP-PAP-TEC1
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8wa0
Q-score: 0.442
Wu XX, Mu WH, Li F, Sun SY, Cui CJ, Kim C, Zhou F, Zhang Y
Cell (2024) 187 pp. 1127-1144.e21 [ DOI: doi:10.1016/j.cell.2024.01.026 Pubmed: 38428393 ]
- Fructokinase-like 2, chloroplastic (72 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 14-like isoform x2 (58 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit beta (120 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit gamma (79 kDa, Protein from Nicotiana tabacum)
- Fe (iii) ion (55 Da, Ligand)
- Protein plastid transcriptionally active 10-like (80 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit beta'' (157 kDa, Protein from Nicotiana tabacum)
- Pap13(ptac18) (17 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 7-like isoform x2 (17 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (34 kDa, Protein from Nicotiana tabacum)
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Udp-n-acetylmuramoyl-l-alanyl-d-glutamate--2, 6-diaminopimelate ligase-like (85 kDa, Protein from Nicotiana tabacum)
- Fructokinase-like 1, chloroplastic (55 kDa, Protein from Nicotiana tabacum)
- Zinc ion (65 Da, Ligand)
- Pentatricopeptide repeat-containing protein at1g74850, chloroplastic-like (96 kDa, Protein from Nicotiana tabacum)
- Pap1(ptac3) (101 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (30 kDa, Protein from Nicotiana tabacum)
- Pap8(ptac6) (38 kDa, Protein from Nicotiana tabacum)
- Nicotiana tabacum pep-pap-tec1 (Complex from Nicotiana tabacum)
- Thioredoxin-like protein citrx1, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Rna (20-mer) (6 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Protein plastid transcriptionally active 12-like (61 kDa, Protein from Nicotiana tabacum)
The cryo-EM structure of the Nicotiana tabacum PEP-PAP-TEC2
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8wa1
Q-score: 0.414
Wu XX, Mu WH, Li F, Sun SY, Cui CJ, Kim C, Zhou F, Zhang Y
Cell (2024) 187 pp. 1127-1144.e21 [ DOI: doi:10.1016/j.cell.2024.01.026 Pubmed: 38428393 ]
- Fructokinase-like 2, chloroplastic (72 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 14-like isoform x2 (58 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit beta (120 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit gamma (79 kDa, Protein from Nicotiana tabacum)
- Fe (iii) ion (55 Da, Ligand)
- Protein plastid transcriptionally active 7-like isoform x1 (19 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 10-like (80 kDa, Protein from Nicotiana tabacum)
- Nicotiana tabacum pep-pap-tec2 (Complex from Nicotiana tabacum)
- Dna-directed rna polymerase subunit beta'' (157 kDa, Protein from Nicotiana tabacum)
- Pap13(ptac18) (17 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (34 kDa, Protein from Nicotiana tabacum)
- Dna (24-mer) (7 kDa, DNA from synthetic construct)
- Udp-n-acetylmuramoyl-l-alanyl-d-glutamate--2, 6-diaminopimelate ligase-like (85 kDa, Protein from Nicotiana tabacum)
- Fructokinase-like 1, chloroplastic (55 kDa, Protein from Nicotiana tabacum)
- Rna (27-mer) (8 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Pentatricopeptide repeat-containing protein at1g74850, chloroplastic-like (96 kDa, Protein from Nicotiana tabacum)
- Pap1(ptac3) (101 kDa, Protein from Nicotiana tabacum)
- Dna (24-mer) (7 kDa, DNA from synthetic construct)
- Pap8(ptac6) (38 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (30 kDa, Protein from Nicotiana tabacum)
- Thioredoxin-like protein citrx1, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Protein plastid transcriptionally active 12-like (61 kDa, Protein from Nicotiana tabacum)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8jch
Q-score: 0.403
Zeng Y, Zhang HW, Wu XX, Zhang Y
Nature (2024) 628 pp. 887-893 [ Pubmed: 38538796 DOI: doi:10.1038/s41586-024-07240-3 ]
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna (7 kDa, RNA from synthetic construct)
- 5'-3' exoribonuclease 2 (117 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna polymerase ii pre-termination complex bound with rat1-rai1 and spt5 (Complex from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Decapping nuclease rai1 (44 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb2 (143 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8k5p
Q-score: 0.412
Zeng Y, Zhang HW, Wu XX, Zhang Y
Nature (2024) 628 pp. 887-893 [ Pubmed: 38538796 DOI: doi:10.1038/s41586-024-07240-3 ]
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription elongation factor spt5 (116 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae S288C)
- 5'-3' exoribonuclease 2 (117 kDa, Protein from Saccharomyces cerevisiae S288C)
- Decapping nuclease rai1 (44 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna polymerase ii pre-termination complex bound with rat1-rai1 and spt5(ptc2) (Complex from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Rna (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb2 (143 kDa, Protein from Saccharomyces cerevisiae S288C)
Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 8h3v
Q-score: 0.191
Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ
Nat Struct Mol Biol (2024) 31 pp. 293-299 [ Pubmed: 38177666 DOI: doi:10.1038/s41594-023-01149-7 ]
- Full transcription activation complex with two activators ntca and ntcb (718 kDa, Complex from Anabaena)
- Dna (125-mer) (38 kDa, DNA from Anabaena)
- Dna-directed rna polymerase subunit gamma (70 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit beta (126 kDa, Protein from Anabaena)
- Dna (125-mer) (38 kDa, DNA from Anabaena)
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit beta' (147 kDa, Protein from Anabaena)
- Rna polymerase sigma factor siga (45 kDa, Protein from Anabaena)
- Ntca (24 kDa, Protein from Anabaena)
- Ntcb (34 kDa, Protein from Anabaena)
Cryo-EM structure of the transcription activation complex NtcA-TAC
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8h40
Q-score: 0.353
Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ
Nat Struct Mol Biol (2024) 31 pp. 293-299 [ Pubmed: 38177666 DOI: doi:10.1038/s41594-023-01149-7 ]
- Dna (125-mer) (38 kDa, DNA from Anabaena)
- Dna-directed rna polymerase subunit gamma (70 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit beta (126 kDa, Protein from Anabaena)
- Dna (125-mer) (38 kDa, DNA from Anabaena)
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit beta' (147 kDa, Protein from Anabaena)
- Transcription activation complex with the global regulator ntca (580 kDa, Complex from Anabaena)
- Rna polymerase sigma factor siga (45 kDa, Protein from Anabaena)
- Ntca (24 kDa, Protein from Anabaena)
A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8hyj
Q-score: 0.205
Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y
Nat Commun (2023) 14 pp. 3118-3118 [ DOI: doi:10.1038/s41467-023-38619-x Pubmed: 37253723 ]
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 4 (22 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii and v subunit 8a (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Arabidopsis thaliana)
- Protein rna-directed dna methylation 3 (158 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase v subunit 7 (20 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase v subunit 1 (218 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Arabidopsis thaliana)
- Ktf1-bound polymerase v transcription elongation complex (608 MDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerase v subunit 5a (25 kDa, Protein from Arabidopsis thaliana)
- Zinc ion (65 Da, Ligand)
- Rna (30-mer) (9 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases iv and v subunit 3b (35 kDa, Protein from Arabidopsis thaliana)
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
Cryo-EM structure of Escherichia coli paused complex of transcription termination (TTC-pause)
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 7yp9
Q-score: 0.345
You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y
Nature (2023) 613 pp. 783-789 [ DOI: doi:10.1038/s41586-022-05604-1 Pubmed: 36631609 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- E. coli paused complex of transcription termination (400 kDa, Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Rna (5'-r(*gp*cp*gp*up*cp*gp*cp*ap*gp*gp*cp*cp*up*up*up*up*up*ap*up*u)-3') (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase (Complex)
- Zinc ion (65 Da, Ligand)
- Dna/rna (Complex)