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 ]
- Pap13(ptac18) (17 kDa, Protein from Nicotiana tabacum)
- Thioredoxin-like protein citrx1, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Pap8(ptac6) (38 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 12-like (61 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 14-like isoform x2 (58 kDa, Protein from Nicotiana tabacum)
- Fructokinase-like 2, chloroplastic (72 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)
- Superoxide dismutase (30 kDa, Protein from Nicotiana tabacum)
- Fe (iii) ion (55 Da, Ligand)
- Fructokinase-like 1, chloroplastic (55 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (34 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Protein plastid transcriptionally active 7-like isoform x1 (19 kDa, Protein from Nicotiana tabacum)
- Udp-n-acetylmuramoyl-l-alanyl-d-glutamate--2, 6-diaminopimelate ligase-like (85 kDa, Protein from Nicotiana tabacum)
- Nicotiana tabacum pep-pap (Complex from Nicotiana tabacum)
- Zinc ion (65 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)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Nicotiana tabacum)
- Pentatricopeptide repeat-containing protein at1g74850, chloroplastic-like (96 kDa, Protein from Nicotiana tabacum)
- Pap1(ptac3) (101 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 ]
- Pap13(ptac18) (17 kDa, Protein from Nicotiana tabacum)
- Thioredoxin-like protein citrx1, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Pap8(ptac6) (38 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 7-like isoform x2 (17 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 12-like (61 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 14-like isoform x2 (58 kDa, Protein from Nicotiana tabacum)
- Rna (20-mer) (6 kDa, RNA from synthetic construct)
- Fructokinase-like 2, chloroplastic (72 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)
- Superoxide dismutase (30 kDa, Protein from Nicotiana tabacum)
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Fe (iii) ion (55 Da, Ligand)
- Fructokinase-like 1, chloroplastic (55 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (34 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Udp-n-acetylmuramoyl-l-alanyl-d-glutamate--2, 6-diaminopimelate ligase-like (85 kDa, Protein from Nicotiana tabacum)
- Nicotiana tabacum pep-pap-tec1 (Complex from Nicotiana tabacum)
- Zinc ion (65 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)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Nicotiana tabacum)
- Pentatricopeptide repeat-containing protein at1g74850, chloroplastic-like (96 kDa, Protein from Nicotiana tabacum)
- Pap1(ptac3) (101 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 ]
- Pap13(ptac18) (17 kDa, Protein from Nicotiana tabacum)
- Pap8(ptac6) (38 kDa, Protein from Nicotiana tabacum)
- Thioredoxin-like protein citrx1, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 12-like (61 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 14-like isoform x2 (58 kDa, Protein from Nicotiana tabacum)
- Fructokinase-like 2, chloroplastic (72 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)
- Superoxide dismutase (30 kDa, Protein from Nicotiana tabacum)
- Dna (24-mer) (7 kDa, DNA from synthetic construct)
- Nicotiana tabacum pep-pap-tec2 (Complex from Nicotiana tabacum)
- Fe (iii) ion (55 Da, Ligand)
- Fructokinase-like 1, chloroplastic (55 kDa, Protein from Nicotiana tabacum)
- Dna (24-mer) (7 kDa, DNA from synthetic construct)
- Superoxide dismutase (34 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Protein plastid transcriptionally active 7-like isoform x1 (19 kDa, Protein from Nicotiana tabacum)
- Udp-n-acetylmuramoyl-l-alanyl-d-glutamate--2, 6-diaminopimelate ligase-like (85 kDa, Protein from Nicotiana tabacum)
- Zinc ion (65 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)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Nicotiana tabacum)
- Rna (27-mer) (8 kDa, RNA from synthetic construct)
- Pentatricopeptide repeat-containing protein at1g74850, chloroplastic-like (96 kDa, Protein from Nicotiana tabacum)
- Pap1(ptac3) (101 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 [ DOI: doi:10.1038/s41586-024-07240-3 Pubmed: 38538796 ]
- Rna (7 kDa, RNA from synthetic construct)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- 5'-3' exoribonuclease 2 (117 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 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 polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Decapping nuclease rai1 (44 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-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb2 (143 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna polymerase ii pre-termination complex bound with rat1-rai1 and spt5 (Complex 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 [ DOI: doi:10.1038/s41586-024-07240-3 Pubmed: 38538796 ]
- Transcription elongation factor spt5 (116 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- 5'-3' exoribonuclease 2 (117 kDa, Protein from Saccharomyces cerevisiae S288C)
- 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 rpb3 (35 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna polymerase ii pre-termination complex bound with rat1-rai1 and spt5(ptc2) (Complex from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 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 polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Decapping nuclease rai1 (44 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-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna (38-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb2 (143 kDa, Protein from Saccharomyces cerevisiae S288C)
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)
- Ktf1-bound polymerase v transcription elongation complex (608 MDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerase v subunit 1 (218 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 polymerase v subunit 5a (25 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 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 6a (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 3b (35 kDa, Protein from Arabidopsis thaliana)
- Rna (30-mer) (9 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase v subunit 7 (20 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii and v subunit 8a (16 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)
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
The cryo-EM structure of C. crescentus GcrA-TACup
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7ye1
Q-score: 0.407
Nucleic Acids Res (2023) [ ]
- Cell cycle regulatory protein gcra (18 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna (Complex)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (154 kDa, Protein from Caulobacter vibrioides NA1000)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit beta (151 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase/gcra/tacup (Complex)
- Dna-directed rna polymerase subunit omega (13 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna (57-mer)-non template (17 kDa, DNA from Caulobacter vibrioides NA1000)
- Dna (57-mer)-template (17 kDa, DNA from Caulobacter vibrioides NA1000)
- Magnesium ion (24 Da, Ligand)
- The cryo-em structure of c. crescentus gcra-tacup (Complex from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Caulobacter vibrioides NA1000)
The cryo-EM structure of C. crescentus GcrA-TACdown
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7ye2
Q-score: 0.354
Nucleic Acids Res (2023) [ ]
- Cell cycle regulatory protein gcra (18 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna (Complex)
- Zinc ion (65 Da, Ligand)
- The cryo-em structure of c. crescentus gcra-tacdown (Complex from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit beta' (154 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase/rpod/gcra (Complex)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit beta (151 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit omega (13 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna (90-mer)-template (27 kDa, DNA from Caulobacter vibrioides NA1000)
- Magnesium ion (24 Da, Ligand)
- Dna (90-mer)-non template (27 kDa, DNA from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Caulobacter vibrioides NA1000)
The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 7eu0
Q-score: 0.487
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y
Science (2021) 374 pp. 1579-1586 [ Pubmed: 34941388 DOI: doi:10.1126/science.abj9184 ]
- Rna (39-mer) (12 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
- Dna (5'-d(*cp*tp*gp*tp*gp*cp*tp*tp*ap*tp*cp*gp*gp*tp*ap*gp*ap*gp*tp*g)-3') (6 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 and iv subunit 5a (24 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Rna-dependent rna polymerase 2 (129 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)
- A. thaliana pol iv-rdr2 backtracked complex (550 kDa, Complex from Arabidopsis thaliana)
- Rna (5'-r(*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- 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 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase iv subunit 1 (169 kDa, Protein from Arabidopsis thaliana)
- Dna (33-mer) (9 kDa, DNA from synthetic construct)
The cryo-EM structure of A. thaliana Pol IV-RDR2 holoenzyme
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 7eu1
Q-score: 0.434
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y
Science (2021) 374 pp. 1579-1586 [ Pubmed: 34941388 DOI: doi:10.1126/science.abj9184 ]
- Zinc ion (65 Da, Ligand)
- 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 and iv subunit 5a (24 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Rna-dependent rna polymerase 2 (129 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)
- Magnesium ion (24 Da, Ligand)
- 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 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- A. thaliana pol iv-rdr2 holoenzyme (Complex from Arabidopsis thaliana)
- Dna-directed rna polymerase iv subunit 1 (169 kDa, Protein from Arabidopsis thaliana)