Complete DNA elongation subcomplex of Xenopus laevis DNA polymerase alpha-primase
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8g9o
Q-score: 0.275
Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF
Nat Struct Mol Biol (2024) 31 pp. 777-790 [ DOI: doi:10.1038/s41594-024-01227-4 Pubmed: 38491139 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Primase (Complex from Xenopus laevis)
- Dna polymerase alpha catalytic subunit (129 kDa, Protein from Xenopus laevis)
- Dna primase large subunit (59 kDa, Protein from Xenopus laevis)
- Polymerase alpha (Complex from Xenopus laevis)
- Dna template (15 kDa, DNA from synthetic construct)
- Rna-dna primer (6 kDa, Macromolecule from synthetic construct)
- 2'-deoxyguanosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna elongation substrate (20 kDa, Complex from synthetic construct)
- Polymerase alpha-primase with a dna elongation substrate (110 kDa, Complex)
Subcomplexes A and E in NDH complex from Arabidopsis
Resolution: 4.33 Å
EM Method: Single-particle
Fitted PDBs: 7wfg
Q-score: 0.232
Su X, Cao D, Pan X, Shi L, Liu Z, Dall'Osto L, Bassi R, Zhang X, Li M
Mol Plant (2022) 15 pp. 454-467 [ DOI: doi:10.1016/j.molp.2022.01.020 Pubmed: 35123031 ]
- Ndht (10 kDa, Protein from Arabidopsis thaliana)
- Iron/sulfur cluster (351 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit h, chloroplastic (45 kDa, Protein from Arabidopsis thaliana)
- Nad(p)h-quinone oxidoreductase subunit i, chloroplastic (20 kDa, Protein from Arabidopsis thaliana)
- Nad(p)h-quinone oxidoreductase subunit m, chloroplastic (24 kDa, Protein from Arabidopsis thaliana)
- Ndho (17 kDa, Protein from Arabidopsis thaliana)
- Subcomplex a and e in ndh complex from arabidopsis (Complex from Arabidopsis thaliana)
- Nad(p)h-quinone oxidoreductase subunit k, chloroplastic (25 kDa, Protein from Arabidopsis thaliana)
- Nad(p)h-quinone oxidoreductase subunit j, chloroplastic (18 kDa, Protein from Arabidopsis thaliana)
- Nad(p)h-quinone oxidoreductase subunit n, chloroplastic (23 kDa, Protein from Arabidopsis thaliana)
- Nad(p)h-quinone oxidoreductase subunit l, chloroplastic (21 kDa, Protein from Arabidopsis thaliana)
PSI-NDH supercomplex of Barley
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7f9o
Q-score: 0.153
Shen L, Tang K, Wang W, Wang C, Wu H, Mao Z, An S, Chang S, Kuang T, Shen JR, Han G, Zhang X
Nature (2022) 601 pp. 649-654 [ DOI: doi:10.1038/s41586-021-04277-6 Pubmed: 34879391 ]
- Photosynthetic ndh subunit of subcomplex b4 (9 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit n, chloroplastic (25 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit k, chloroplastic (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 3, chloroplastic (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Psi-ndh supercomplex of barley (Complex from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit iii, chloroplastic (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Unidentified stromal protein (5 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca4 (21 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit l, chloroplastic (22 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit vi, chloroplastic (14 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit iv, chloroplastic (15 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit m, chloroplastic (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nadh-plastoquinone oxidoreductase subunit 5 (87 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b3 (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b5 (18 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b2 (38 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l1 (17 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit ii, chloroplastic (21 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit xi, chloroplastic (22 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l4 (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca5 (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll b (907 Da, Ligand)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Photosynthetic ndh subunit of subcomplex b1 (51 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l2 (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 2, chloroplastic (53 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 4l, chloroplastic (11 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 6, chloroplastic (19 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 1, chloroplastic (38 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase chain 4, chloroplastic (56 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit j, chloroplastic (18 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca1 (26 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit psak, chloroplastic (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l5 (25 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit i, chloroplastic (19 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit h, chloroplastic (44 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l2 (23 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a isomer (893 Da, Ligand)
Structure of yeast DNA Polymerase Zeta (apo)
Resolution: 4.11 Å
EM Method: Single-particle
Fitted PDBs: 7lxd
Q-score: 0.23
Du Truong C, Craig TA, Cui G, Botuyan MV, Serkasevich RA, Chan KY, Mer G, Chiu PL, Kumar R
J Biol Chem (2021) 297 pp. 100912-100912 [ DOI: doi:10.1016/j.jbc.2021.100912 Pubmed: 34174285 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase zeta catalytic subunit (173 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta (172 MDa, Complex from Saccharomyces cerevisiae S288C)
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)
Resolution: 4.07 Å
EM Method: Single-particle
Fitted PDBs: 7ena
Q-score: 0.168
Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y
Science (2021) 372 [ Pubmed: 33958484 DOI: doi:10.1126/science.abg0635 ]
- Dna-directed rna polymerase (Complex)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Pig)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Tfiid-based pic-mediator holo-complex in pre-assembled state (pre-hpic-med) (Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Tfiih (Complex from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Dna(69-mer) (21 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Tfiid (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Dna (69-mer) (21 kDa, DNA from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Mediator (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Tfiif (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rpb1 (217 kDa, Protein from Pig)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 26 (65 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Pig)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 1 (168 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Tfiia-a (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
Resolution: 4.13 Å
EM Method: Single-particle
Fitted PDBs: 7enc
Q-score: 0.103
Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y
Science (2021) 372 [ Pubmed: 33958484 DOI: doi:10.1126/science.abg0635 ]
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Dna (69-mer) (21 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Pig)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 26 (65 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 1 (168 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Dna (69-mer) (21 kDa, DNA from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Tfiia-a (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Tfiid-based pic-mediator holo-complex in fully-assembled state (hpic-med) (Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
Structure of the human Mediator-bound transcription pre-initiation complex
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7lbm
Q-score: 0.074
Abdella R, Talyzina A, Chen S, Inouye CJ, Tjian R, He Y
Science (2021) 372 pp. 52-56 [ DOI: doi:10.1126/science.abg3074 Pubmed: 33707221 ]
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Human)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Human)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Human)
- General transcription factor iih subunit 2 (44 kDa, Protein from Human)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Human)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Human)
- Promoter dna (Complex from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Human)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Human)
- General transcription factors (300 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Human)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Human)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Human)
- General transcription factor iih subunit 5 (8 kDa, Protein from Human)
- General transcription factor iih subunit 3 (34 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Human)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Human)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Human)
- Mediator (1 MDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Human)
- Zinc ion (65 Da, Ligand)
- Super core promoter sense strand (31 kDa, DNA from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Human)
- Tfiih (500 kDa, Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Human)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Human)
- Super core promoter antisense strand (30 kDa, DNA from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Human)
- General transcription factor iih subunit 1 (62 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Human)
- Cyclin-h and associated factors (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Human)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Human)
- Iron/sulfur cluster (351 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Human)
- Mediator-bound pre-initiation complex (2 MDa, Complex)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Human)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Human)
- Rna polymerase ii (520 kDa, Complex from Homo sapiens)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6u8y
Q-score: 0.414
Yu H, Haja DK, Schut GJ, Wu CH, Meng X, Zhao G, Li H, Adams MWW
Nat Commun (2020) 11 pp. 5953-5953 [ DOI: doi:10.1038/s41467-020-19697-7 Pubmed: 33230146 ]
- Duf4040 domain-containing protein (10 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit n (53 kDa, Protein from Pyrococcus furiosus COM1)
- Iron/sulfur cluster (351 Da, Ligand)
- Monovalent cation/h+ antiporter subunit c (12 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit g (13 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit c (20 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit (33 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit b (25 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit i (24 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit e (19 kDa, Protein from Pyrococcus furiosus COM1)
- Monovalent cation/h+ antiporter subunit f (9 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit b (22 kDa, Protein from Pyrococcus furiosus COM1)
- Nadh dehydrogenase subunit m (67 kDa, Protein from Pyrococcus furiosus COM1)
- Respiratory membrane complex (Complex from Pyrococcus furiosus)
- Nadh dehydrogenase subunit d (44 kDa, Protein from Pyrococcus furiosus COM1)
Structure of DNA Polymerase Zeta (Apo)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6v8p
Q-score: 0.369
Malik R, Kopylov M, Gomez-Llorente Y, Jain R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK
Nat Struct Mol Biol (2020) 27 pp. 913-924 [ DOI: doi:10.1038/s41594-020-0476-7 Pubmed: 32807989 ]
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta catalytic subunit (177 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Apo (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cryo-EM structure of respiratory complex I from Yarrowia lipolytica
Resolution: 4.32 Å
EM Method: Single-particle
Fitted PDBs: 6gcs
Q-score: 0.371
Parey K, Brandt U, Xie H, Mills DJ, Siegmund K, Vonck J, Kuehlbrandt W, Zickermann V
eLife (2018) 7 [ DOI: doi:10.7554/eLife.39213 Pubmed: 30277212 ]
- Flavin mononucleotide (456 Da, Ligand)
- Nunm subunit (7 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Acpm1 subunit (12 kDa, Protein from Yarrowia lipolytica)
- Nuum subunit (3 kDa, Protein from Yarrowia lipolytica)
- Mitochondrial nadh:ubiquinone oxidoreductase (963 MDa, Complex from Yarrowia lipolytica)
- 49-kda protein (nucm) (52 kDa, Protein from Yarrowia lipolytica)
- Ni2m subunit (12 kDa, Protein from Yarrowia lipolytica)
- Nuxm subunit (18 kDa, Protein from Yarrowia lipolytica)
- 1,2-diacyl-sn-glycero-3-phosphoethanolamine (748 Da, Ligand)
- Nebm subunit (5 kDa, Protein from Yarrowia lipolytica)
- Acpm2 subunit (14 kDa, Protein from Yarrowia lipolytica)
- 24-kda subunit (nuhm) (27 kDa, Protein from Yarrowia lipolytica)
- Nb5m subunit (10 kDa, Protein from Yarrowia lipolytica)
- Unknown subunit (4 kDa, Protein from Yarrowia lipolytica)
- Nipm subunit (10 kDa, Protein from Yarrowia lipolytica)
- Nb8m subunit (11 kDa, Protein from Yarrowia lipolytica)
- Nesm subunit (13 kDa, Protein from Yarrowia lipolytica)
- N7bm subunit (16 kDa, Protein from Yarrowia lipolytica)
- Nufm subunit (16 kDa, Protein from Yarrowia lipolytica)
- Niam subunit (8 kDa, Protein from Yarrowia lipolytica)
- Numm subunit (15 kDa, Protein from Yarrowia lipolytica)
- Nidm subunit (11 kDa, Protein from Yarrowia lipolytica)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nupm subunit (19 kDa, Protein from Yarrowia lipolytica)
- 30-kda protein (nugm) (32 kDa, Protein from Yarrowia lipolytica)
- Nuym subunit (18 kDa, Protein from Yarrowia lipolytica)
- Nd3 subunit (nu3m) (14 kDa, Protein from Yarrowia lipolytica)
- Nujm subunit (20 kDa, Protein from Yarrowia lipolytica)
- Iron/sulfur cluster (351 Da, Ligand)
- Nimm subunit (9 kDa, Protein from Yarrowia lipolytica)
- Nd4 subunit (nu4m) (54 kDa, Protein from Yarrowia lipolytica)
- S-[2-({n-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate (568 Da, Ligand)
- Nuzm subunit (11 kDa, Protein from Yarrowia lipolytica)
- Tyky subunit (nuim) (25 kDa, Protein from Yarrowia lipolytica)
- Nd4l subunit (nulm) (9 kDa, Protein from Yarrowia lipolytica)
- Psst subunit (nukm) (23 kDa, Protein from Yarrowia lipolytica)
- Ni9m subunit (7 kDa, Protein from Yarrowia lipolytica)
- Nd2 subunit (nu2m) (53 kDa, Protein from Yarrowia lipolytica)
- Zinc ion (65 Da, Ligand)
- Nuem subunit (42 kDa, Protein from Yarrowia lipolytica)
- Nb4m subunit (14 kDa, Protein from Yarrowia lipolytica)
- 51-kda protein (nubm) (53 kDa, Protein from Yarrowia lipolytica)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Nb6m subunit (14 kDa, Protein from Yarrowia lipolytica)
- Nd1 subunit (nu1m) (38 kDa, Protein from Yarrowia lipolytica)
- Nd5 subunit (nu5m) (73 kDa, Protein from Yarrowia lipolytica)
- Nd6 subunit (nu6m) (20 kDa, Protein from Yarrowia lipolytica)
- Ni8m subunit (9 kDa, Protein from Yarrowia lipolytica)
- Nb2m subunit (6 kDa, Protein from Yarrowia lipolytica)
- 75-kda protein (nuam) (79 kDa, Protein from Yarrowia lipolytica)