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EMBL

was set up in 1974 as Europe’s flagship laboratory for the life sciences – an intergovernmental organisation with more than 80 independent research groups covering the spectrum of molecular biology:

Research:

perform basic research in molecular biology

Services:

offer vital services to scientists in the member states

Training

scientists, students and visitors at all levels

Transfer

and development of technology

Develop

new instruments and methods

Integrating

life science research in Europe

More about EMBL

Six sites

represent EMBL in Europe.

Barcelona

Tissue biology and disease modelling

Grenoble

Structural biology

Hamburg

Structural biology

Heidelberg

Main laboratory

Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

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sample_name:"subunit f" AND author_name:"Li" AND xref_links:"cpx" AND resolution:[4 TO 5}

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EMD-37353

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human co-transcriptional RNA capping enzyme RNGTT-CMTR1

Release date: April 10, 2024
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8w8f
Q-score: 0.228

Li Y, Wang Q, Xu Y, Li Z

Nat Commun (2024) 15 pp. 4622-4622 [ Pubmed: 38816438 DOI: doi:10.1038/s41467-024-48963-1 ]

Sample:

Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
Dna (45-mer) (14 kDa, DNA from Homo sapiens)
Transcription elongation factor, m-rna capping enzyme, cmtr1 (Complex from Homo sapiens)
Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
Dna-rna (Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
Rpb12 (7 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase (Complex from Sus scrofa)
Zinc ion (65 Da, Ligand)
Human co-transcriptional rna capping enzyme rngtt-cmtr1 (Complex)
Dna (36-mer) (14 kDa, DNA from Homo sapiens)
Rna (5'-r(p*gp*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)

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EMD-31204

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TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)

Release date: May 26, 2021
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 [ DOI: doi:10.1126/science.abg0635 Pubmed: 33958484 ]

Sample:

Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
Tfiia-a (34 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
Mediator (Complex from Homo sapiens)
Tfiib (Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
Tfiid (Complex from Sus scrofa)
Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
Iron/sulfur cluster (351 Da, Ligand)
Dna (Complex)
Tfiid-based pic-mediator holo-complex in pre-assembled state (pre-hpic-med) (Complex from Homo sapiens)
Tfiif (Complex from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
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 Sus scrofa)
Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
Tfiih (Complex from Homo sapiens)
Tfiie (Complex from Homo sapiens)
Zinc ion (65 Da, Ligand)
Dna (69-mer) (21 kDa, DNA from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
General transcription factor iif subunit 2 (28 kDa, Protein 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)
Rpb10 (7 kDa, Protein from Sus scrofa)
Rpb12 (7 kDa, Protein from Sus scrofa)
Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase (Complex)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
Mediator of rna polymerase ii transcription subunit 26 (65 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 9 (16 kDa, Protein from Homo sapiens)
General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
Cyclin-h (37 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 22 (22 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)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
Dna(69-mer) (21 kDa, DNA from Homo sapiens)
Tfiia (Complex from Homo sapiens)
Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 1 (168 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 18 (23 kDa, Protein from Homo sapiens)
Rpb1 (217 kDa, Protein from Sus scrofa)
Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)

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EMD-31075

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p53-bound TFIID-based core PIC on HDM2 promoter

Release date: May 5, 2021
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 ]

Sample:

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)

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EMD-31110

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TFIID-based intermediate PIC on PUMA promoter

Release date: May 5, 2021
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7ega
Q-score: 0.122

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 ]

Sample:

General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
Rna polymerase ii (Complex from Sus scrofa)
Dna (85-mer) (26 kDa, DNA from Homo sapiens)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Dna (85-mer) (26 kDa, DNA from Homo sapiens)
Dna-directed rna polymerase subunit (167 kDa, Protein from Sus scrofa)
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)
Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
Tfiia (Complex from Homo sapiens)
Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
Dna(puma promoters) (Complex)
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)
Tfiie (Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
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)
Tfiid-based intermediate pic on puma promoter (Complex)
Transcription initiation factor tfiid subunit 4 (110 kDa, Protein 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)

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EMDB [4]

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