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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 xref_links:"cpx" AND author_orcid:"0000-0003-2416-9153" AND sample_type:"ligand"

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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-16610

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Yeast RNA polymerase II transcription pre-initiation complex with core Mediator

Release date: March 22, 2023
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8cen
Q-score: 0.269

Schilbach S, Wang H, Dienemann C, Cramer P

PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]

Sample:

Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from baker's yeast)
Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from baker's yeast)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from baker's yeast)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from baker's yeast)
Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from baker's yeast)
Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from baker's yeast)
Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
Dna (Complex from Synthetic construct)
Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from baker's yeast)
Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
Yeast rna polymerase ii transcription pre-initiation complex with core mediator (2 MDa, Complex)
General transcription and dna repair factors, and rna polymerase ii transcription factor b subunit 3 (Complex from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
Dna-directed rna polymerase subunits (Complex from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from baker's yeast)
Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factors and mediator of rna polymerase ii transcription subunits (Complex from Saccharomyces cerevisiae)
Iron/sulfur cluster (351 Da, Ligand)
Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from baker's yeast)
Mediator of rna polymerase ii transcription subunit 14 (84 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from baker's yeast)
Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from baker's yeast)
General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from baker's yeast)
Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
Template dna (209-mer) (64 kDa, DNA from synthetic construct)
General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)

[Show more]

Sort by: Download

Showing 1 - 3 of 3. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [3]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

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Field: