Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 9c9w
Q-score: 0.198
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Manganese (ii) ion (54 Da, Ligand)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*cp*ap*gp*ap*tp*cp*ap*gp*ap*ap*tp*gp*ap*ap*tp*ap*tp*ap*cp*tp*ap*ap*a)-3') (7 kDa, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(*ap*tp*tp*gp*gp*ap*gp*tp*tp*cp*ap*tp*gp*tp*gp*ap*tp*gp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna (38-mer) (12 kDa, DNA from Homo sapiens)
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Dimerized human top3b-tdrd3 core complexes with a dna mismatch bubble (Complex from Homo sapiens)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8sna
Q-score: 0.405
Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G
Mol Cell (2024) 84 pp. 839-853.e12 [ DOI: doi:10.1016/j.molcel.2023.12.036 Pubmed: 38242129 ]
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Human nucleosome core particle in complex with rnf168 and ubch5c~ub (with backside ub) (256 kDa, Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7wbv
Q-score: 0.267
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ Pubmed: 37120012 DOI: doi:10.1016/j.jmb.2023.168130 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*up*gp*gp*cp*cp*gp*up*up*up*up*cp*gp*up*up*gp*u)-3') (5 kDa, RNA from synthetic construct)
- Transcription elongation factor spt5 (91 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (159-mer) (60 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna, rna (Complex)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-4) of the nucleosome (Complex from Komagataella phaffii)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7wbx
Q-score: 0.298
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ Pubmed: 37120012 DOI: doi:10.1016/j.jmb.2023.168130 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*cp*gp*up*up*gp*up*up*up*up*up*up*up*cp*up*g)-3') (4 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna, rna (Complex)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-3) of the nucleosome (Complex from Komagataella pastoris)
Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase core
Resolution: 4.08 Å
EM Method: Single-particle
Fitted PDBs: 7z8q
Q-score: 0.307
Morichaud Z, Trapani S, Vishwakarma RK, Chaloin L, Lionne C, Lai-Kee-Him J, Bron P, Brodolin K
Nat Commun (2023) 14 pp. 484- [ DOI: doi:10.1038/s41467-023-36113-y ]
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (129 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (147 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-dependent rna polymerase core (400 kDa, Complex from Mycobacterium tuberculosis H37Rv)
In situ double-PBS-PSII-PSI-LHCs megacomplex from Porphyridium purpureum.
You X, Zhang X, Cheng J, Xiao Y, Ma J, Sun S, Zhang X, Wang HW, Sui SF
Nature (2023) 616 pp. 199-206 [ Pubmed: 36922595 DOI: doi:10.1038/s41586-023-05831-0 ]
- B-phycoerythrin beta chain (18 kDa, Protein from Porphyridium purpureum)
- In situ double-pbs-psii-psi-lhcs megacomplex from porphyridium purpureum. (Cell from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Porphyridium purpureum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Carsp2 (15 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein of lhcii type iii, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i subunit o (9 kDa, Protein from Porphyridium purpureum)
- Ferredoxin (10 kDa, Protein from Porphyridium purpureum)
- Carsp1 (24 kDa, Protein from Porphyridium purpureum)
- Cytochrome c6 (8 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (39 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein t (3 kDa, Protein from Porphyridium purpureum)
- Lrc5 (30 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit psak (6 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin beta subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein d1 (39 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (29 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein l (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Redcap (19 kDa, Protein from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Phycourobilin (590 Da, Ligand)
- (2s)-2,3-dihydroxypropyl octadecanoate (358 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp43 reaction center protein (52 kDa, Protein from Porphyridium purpureum)
- Lpp2 (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center x protein (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Oxygen-evolving enhancer protein (30 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Porphyridium purpureum)
- Phycobiliprotein apce (99 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Porphyridium purpureum)
- Fucoxanthin-chlorophyll a-c binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xi (14 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (36 kDa, Protein from Porphyridium purpureum)
- Phycoerythrin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Psii_pbs31 domain-containing protein (22 kDa, Protein from Porphyridium purpureum)
- Fe (iii) ion (55 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Lr6 (46 kDa, Protein from Porphyridium purpureum)
- Psar (12 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Porphyridium purpureum)
- Lrh (20 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Porphyridium purpureum)
- Linker4 (11 kDa, Protein from Porphyridium purpureum)
- Psbm (10 kDa, Protein from Porphyridium purpureum)
- Beta-carotene (536 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (37 kDa, Protein from Porphyridium purpureum)
- Psb34 (2 kDa, Protein from Porphyridium purpureum)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Glycerol (92 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein y (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein k (5 kDa, Protein from Porphyridium purpureum)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Phycoerythrobilin (588 Da, Ligand)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (10 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (31 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Porphyridium purpureum)
- Water (18 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (53 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin gamma subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (26 kDa, Protein from Porphyridium purpureum)
- Psbw (3 kDa, Protein from Porphyridium purpureum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lpp1 (10 kDa, Protein from Porphyridium purpureum)
- Ps ii complex 12 kda extrinsic protein (16 kDa, Protein from Porphyridium purpureum)
- Cytochrome c550 (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein h (7 kDa, Protein from Porphyridium purpureum)
- Lrc4 (16 kDa, Protein from Porphyridium purpureum)
- Lps1 (5 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (34 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (55 kDa, Protein from Porphyridium purpureum)
- Beta-d-glucopyranose (180 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Porphyridium purpureum)
- Photosystem ii d2 protein (39 kDa, Protein from Porphyridium purpureum)
- Cnt (10 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein j (3 kDa, Protein from Porphyridium purpureum)
- Psbq' (22 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (27 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit beta (5 kDa, Protein from Porphyridium purpureum)
- Psab (82 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta subunit (17 kDa, Protein from Porphyridium purpureum)
RNA polymerase II transcribing a chromatosome (type II)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8h0w
Q-score: 0.16
Hirano R, Ehara H, Kujirai T, Uejima T, Takizawa Y, Sekine SI, Kurumizaka H
Nat Commun (2022) 13 pp. 7287-7287 [ DOI: doi:10.1038/s41467-022-35003-z Pubmed: 36435862 ]
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*cp*ap*ap*up*ap*gp*gp*ap*gp*cp*up*up*ap*c)-3') (4 kDa, RNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h1.2 (22 kDa, Protein from Homo sapiens)
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Komagataella phaffii)
- Histone (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii transcribing a chromatosome (type ii) (Complex)
- Dna, rna (Complex)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
RNA polymerase II elongation complex transcribing a nucleosome (EC49B)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7xt7
Q-score: 0.207
Ehara H, Kujirai T, Shirouzu M, Kurumizaka H, Sekine SI
Science (2022) 377 pp. eabp9466-eabp9466 [ DOI: doi:10.1126/science.abp9466 Pubmed: 35981082 ]
- Leo1 (52 kDa, Protein from Komagataella phaffii)
- Constituent of paf1 complex with rna polymerase ii, paf1p, hpr1p, ctr9, leo1, rtf1 and ccr4p (44 kDa, Protein from Komagataella phaffii)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna, rna (Complex from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Spt4,spt5, paf1p,spt16,pob3 (Complex from Komagataella phaffii)
- Spt6 (Complex from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Protein that interacts with spt6p and copurifies with spt5p and rna polymerase ii (46 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Component of the paf1p complex (124 kDa, Protein from Komagataella phaffii)
- Fact complex subunit (115 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Transcription elongation factor spt6 (173 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii elongation complex transcribing a nucleosome (ec49b) (Complex)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rnapii-associated chromatin remodeling paf1 complex subunit (62 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rnap ii-associated protein (46 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*ap*cp*cp*cp*gp*gp*gp*up*gp*up*cp*up*up*cp*cp*cp*cp*a)-3') (6 kDa, RNA from synthetic construct)
- Fact complex subunit pob3 (60 kDa, Protein from Komagataella phaffii)
Cryo-EM structure of 7SK core RNP with linear RNA
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7slp
Q-score: 0.224
Yang Y, Liu S, Egloff S, Eichhorn CD, Hadjian T, Zhen J, Kiss T, Zhou ZH, Feigon J
Mol Cell (2022) 82 pp. 1724- [ DOI: doi:10.1016/j.molcel.2022.03.001 Pubmed: 35320752 ]
- La-related protein 7 (55 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- 7sk snrna methylphosphate capping enzyme, la-related protein 7 (Complex from Homo sapiens)
- 7sk snrna methylphosphate capping enzyme (35 kDa, Protein from Homo sapiens)
- Rna (Complex)
- Linear 7sk rna (26 kDa, RNA from Homo sapiens)
- 7sk linear core rnp with mepce,larp7 and linear 7sk rna (Complex)
p53-bound TFIID-based core PIC on HDM2 promoter
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7edx
Q-score: 0.13
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna(scp promoters) (Complex)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Dna (84-mer) (26 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- P53-bound tfiid-based core pic on hdm2 promoter (Complex)
- Dna (84-mer) (25 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)