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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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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- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]

Sample:

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)
Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
Nucleosome (protein) (Complex from Xenopus laevis)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
Tata-box binding protein (Complex from Homo sapiens)
Template dna (67 kDa, DNA from unidentified adenovirus)
Dna-directed rna polymerase subunit (217 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)
General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
Non-template dna (67 kDa, DNA from unidentified adenovirus)
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)
General transcription factor iia (Complex from Homo sapiens)
General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
General transcription factor iie (Complex from Homo sapiens)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
General transcription factor iif (Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
Nucleosome (dna) (Complex from unidentified adenovirus)
Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
Cyclin-h (37 kDa, Protein from Homo sapiens)
Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
Iron/sulfur cluster (351 Da, Ligand)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
General transcription factor iih (490 kDa, Complex from Homo sapiens)
General transcription factor iib (Complex from Homo sapiens)
Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
General transcription and dna repair factor iih helicase subunit xpb (88 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- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]

Sample:

Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
Nucleosome (protein) (Complex from Xenopus laevis)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
Tata-box binding protein (Complex from Homo sapiens)
Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
Template dna (64 kDa, DNA from unidentified adenovirus)
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)
General transcription factor iih (Complex from Homo sapiens)
General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
General transcription factor iia (Complex from Homo sapiens)
General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
General transcription factor iie (Complex from Homo sapiens)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
General transcription factor iif (Complex from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
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)
Zinc ion (65 Da, Ligand)
Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
Nucleosome (dna) (Complex from unidentified adenovirus)
Mammalian rna polymerase ii (Complex from Sus scrofa)
Cyclin-h (37 kDa, Protein from Homo sapiens)
Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
Iron/sulfur cluster (351 Da, Ligand)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
General transcription factor iib (Complex from Homo sapiens)
Non-template dna (64 kDa, DNA from unidentified adenovirus)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)

[Show more]

EMD-23905

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RNA polymerase II pre-initiation complex (PIC2)

Release date: Feb. 2, 2022
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7ml1
Q-score: 0.291

Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K

Mol Cell (2022) 82 pp. 660-676.e9 [ Pubmed: 35051353 DOI: doi:10.1016/j.molcel.2021.12.020 ]

Sample:

Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
Dna+tfiia+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
Template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
Tfb1 (58 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
Non-template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
Iron/sulfur cluster (351 Da, Ligand)
Tfiih (Complex from Saccharomyces cerevisiae)
Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
Rna polymerase ii pre-initiation complex (pic2) (Complex from Saccharomyces cerevisiae)

[Show more]

EMD-3846

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STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH

Release date: April 25, 2018
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 5oqj
Q-score: 0.249

Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P

Nature (2017) 551 pp. 204-209 [ Pubmed: 29088706 DOI: doi:10.1038/nature24282 ]

Sample:

Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna repair helicase rad25 (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Transcription initiation factor iie subunit alpha (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Initiation factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Magnesium ion (24 Da, Ligand)
Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Transcription factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Unknown protein (3 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Rna polymerase ii transcription factor b subunit 1 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Pre-initiation complex (pic) (1 MDa, Complex)
Polymerase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Rna polymerase ii transcription factor b subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Suppressor of stem-loop protein 1 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Nontemplate dna (32 kDa, DNA from synthetic construct)
Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Template dna (32 kDa, DNA from synthetic construct)
Nucleic acid (Complex from synthetic construct)
Rna polymerase ii transcription factor b subunit 2 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Iron/sulfur cluster (351 Da, Ligand)
Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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