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)
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)
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 6j9e
Q-score: 0.451
You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W, Feng Y, Zhang Y
Nat Commun (2019) 10 pp. 3048-3048 [ DOI: doi:10.1038/s41467-019-10955-x Pubmed: 31296855 ]
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Xanthomonas oryzae pv. oryzae (strain PXO99A))
- Dna (29-mer) (8 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (154 kDa, Protein from Xanthomonas oryzae pv. oryzae PXO99A)
- Xoo transcription elongation complex with p7 and nusa (p7-nusa-tec) (480 kDa, Complex from Xanthomonas oryzae pv. oryzae)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Xanthomonas oryzae pv. oryzae)
- 45l (8 kDa, Protein from Xanthomonas virus Xp10)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Xanthomonas oryzae pv. oryzae PXO99A)
- Magnesium ion (24 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from synthetic construct)
- Transcription termination/antitermination protein nusa (55 kDa, Protein from Xanthomonas oryzae pv. oryzae PXO99A)
- Rna (5'-r(*gp*cp*ap*up*up*cp*ap*ap*ap*gp*cp*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from synthetic construct)
Resolution: 3.95 Å
EM Method: Single-particle
Fitted PDBs: 6j9f
Q-score: 0.418
You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W, Feng Y, Zhang Y
Nat Commun (2019) 10 pp. 3048-3048 [ DOI: doi:10.1038/s41467-019-10955-x Pubmed: 31296855 ]
- Dna (29-mer) (8 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (154 kDa, Protein from Xanthomonas oryzae pv. oryzae MAFF 311018)
- Dna (29-mer) (8 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Xanthomonas oryzae pv. oryzae)
- 45l (8 kDa, Protein from Xanthomonas virus Xp10)
- Rna (5'-r(p*ap*gp*cp*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Xanthomonas oryzae pv. oryzae PXO99A)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Xanthomonas oryzae pv. oryzae PXO99A)
- Magnesium ion (24 Da, Ligand)
- Xoo transcription elongation complex with p7(p7-tec) (427 kDa, Complex from Xanthomonas oryzae)