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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:"IRON/SULFUR CLUSTER" AND resolution:[4 TO 5} AND sample_type:"protein" AND natural_source_ncbi_code:"9606" AND natural_source_ncbi_code:"8355"

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EMD-16274

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RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)

Release date: May 3, 2023
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234

Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P

Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]

Sample:

General transcription factor iih (490 kDa, Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
Rna polymerase ii subunit k (7 kDa, Protein from pig)
Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
Rna polymerase ii subunit d (16 kDa, Protein from pig)
General transcription factor iih subunit 1 (62 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)
General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
General transcription factor iif (Complex from Homo sapiens)
Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
Tata-box binding protein (Complex from Homo sapiens)
Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
Zinc ion (65 Da, Ligand)
Dna-directed rna polymerase subunit (217 kDa, Protein from pig)
Non-template dna (67 kDa, DNA from unidentified adenovirus)
Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
Nucleosome (protein) (Complex from Xenopus laevis)
General transcription factor iie (Complex from Homo sapiens)
Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Magnesium ion (24 Da, Ligand)
Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Iron/sulfur cluster (351 Da, Ligand)
Cyclin-h (37 kDa, Protein from Homo sapiens)
Nucleosome (dna) (Complex from unidentified adenovirus)
General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
General transcription factor iib (Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit f (14 kDa, Protein from pig)
Template dna (67 kDa, DNA from unidentified adenovirus)
General transcription factor iia (Complex from Homo sapiens)
General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)

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EMD-16331

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RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)

Release date: May 3, 2023
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8byq
Q-score: 0.187

Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P

Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]

Sample:

Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
General transcription factor iih (Complex from Homo sapiens)
Rna polymerase ii subunit k (7 kDa, Protein from pig)
Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
Rna polymerase ii subunit d (16 kDa, Protein from pig)
General transcription factor iih subunit 1 (62 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)
General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
General transcription factor iif (Complex from Homo sapiens)
Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
Tata-box binding protein (Complex from Homo sapiens)
Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
Zinc ion (65 Da, Ligand)
General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase subunit (217 kDa, Protein from pig)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
Mammalian rna polymerase ii (Complex from Sus scrofa)
Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
Nucleosome (protein) (Complex from Xenopus laevis)
General transcription factor iie (Complex from Homo sapiens)
Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
Non-template dna (64 kDa, DNA from unidentified adenovirus)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Template dna (64 kDa, DNA from unidentified adenovirus)
Magnesium ion (24 Da, Ligand)
Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Iron/sulfur cluster (351 Da, Ligand)
Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
Cyclin-h (37 kDa, Protein from Homo sapiens)
Nucleosome (dna) (Complex from unidentified adenovirus)
General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
General transcription factor iib (Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit f (14 kDa, Protein from pig)
General transcription factor iia (Complex from Homo sapiens)
General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)

[Show more]

EMD-34360

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PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state

Release date: Nov. 2, 2022
Resolution: 4.16 Å
EM Method: Single-particle
Fitted PDBs: 8gxs
Q-score: 0.093

Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y

Science (2022) 378 pp. 62-68 [ DOI: doi:10.1126/science.abn8131 Pubmed: 36201575 ]

Sample:

Dna (228-mer) (70 kDa, DNA from synthetic construct)
Dna-directed rna polymerase ii subunit rpb7 (19 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 19 (26 kDa, Protein from Homo sapiens)
Pic-mediator in complex with +1 nucleosome (t40n) in h-binding state (Complex from Homo sapiens)
Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
Dna (162-mer) (53 kDa, DNA from synthetic construct)
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)
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)
Histone h2b (13 kDa, Protein from Xenopus laevis)
General transcription and dna repair factor iih helicase subunit xpd (87 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)
Iron/sulfur cluster (351 Da, Ligand)
Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
Mediator of rna polymerase ii transcription subunit 31 (15 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 27 (35 kDa, Protein from Homo sapiens)
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)
Histone h3 (15 kDa, Protein from Xenopus laevis)
Dna (162-mer) (46 kDa, DNA from synthetic construct)
Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
Tata-box-binding protein (37 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)
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)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
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)
Cyclin-dependent kinase 7 (39 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)
Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
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)
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)
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)
Rpb12 (7 kDa, Protein from Sus scrofa)
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)
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 (228-mer) (70 kDa, DNA from synthetic construct)
Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
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)
Histone h2a.z (13 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)

[Show more]

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Display: Statistics

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EMDB [3]

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Select the script type:

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