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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-d" AND microscope_name:"TFS KRIOS" AND database:"EMDB" AND xref_links:"cpx"

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EMD-15007

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Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC)

Release date: Dec. 7, 2022
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7zx8
Q-score: 0.356

Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P

Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ Pubmed: 36424526 DOI: doi:10.1038/s41594-022-00857-w ]

Sample:

Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Snrna-activating protein complex subunit 5 (11 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)
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)
Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
Template strand (29 kDa, DNA from Homo sapiens)
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)
Snapc (Complex from Homo sapiens)
Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
Rna polymerase ii (Complex from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
Promoter (Complex from Sus scrofa)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
Non-template strand (29 kDa, DNA from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
Zinc ion (65 Da, Ligand)
Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Pre-initiation complex of rna polymerase ii with general transcription factors and snapc bound to u1 promoter (Complex)

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EMD-14997

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Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC)

Release date: Nov. 30, 2022
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7zwd
Q-score: 0.342

Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P

Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ Pubmed: 36424526 DOI: doi:10.1038/s41594-022-00857-w ]

Sample:

Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Snrna-activating protein complex subunit 5 (11 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)
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)
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)
Snapc (Complex from Homo sapiens)
Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
Rna polymerase ii (Complex from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
Pre-initiation complex of rna polymerase ii with general transcription factors and snapc bound to u5 promoter (Complex)
Promoter (Complex 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)
Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
Zinc ion (65 Da, Ligand)
Template strand (29 kDa, DNA from Homo sapiens)
Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Non-template strand (29 kDa, DNA from Homo sapiens)
Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)

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EMD-15006

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Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC)

Release date: Nov. 30, 2022
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7zx7
Q-score: 0.267

Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P

Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ Pubmed: 36424526 DOI: doi:10.1038/s41594-022-00857-w ]

Sample:

Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Snrna-activating protein complex subunit 5 (11 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)
Rna polymerase ii (Complex from Sus scrofa)
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)
Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
Template strand (29 kDa, DNA from Homo sapiens)
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)
Snapc (Complex from Homo sapiens)
Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
Non-template strand (29 kDa, DNA from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
Zinc ion (65 Da, Ligand)
Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Promoter (Complex from Homo sapiens)
Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Pre-initiation complex of rna polymerase ii with general transcription factors and snapc bound to u1 promoter (Complex)

[Show more]

EMD-31538

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CryoEM Structure of Reconstituted V-ATPase, state1

Release date: Dec. 22, 2021
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7fda
Q-score: 0.205

Khan MM, Lee S, Oot RA, Couoh-Cardel S, Kim H, Wilkens S, Roh SH

EMBO J (2021) [ ]

Sample:

V-type proton atpase subunit c (44 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit b (57 kDa, Protein from Saccharomyces cerevisiae S288C)
Chimeric subunit h (Complex from Saccharomyces cerevisiae S288c)
Yeast vacuolar atpase f subunit (9 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase in rotary state 1 (1 MDa, Complex from Saccharomyces cerevisiae S288c)
Fusion of yeast v-type proton atpase subunit h(nt) and human v-type proton atpase subunit h(ct) (53 kDa, Protein from Homo sapiens)
V-type proton atpase subunit d (29 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit g (13 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit e (26 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast v-type proton atpase subunit c (Complex from Saccharomyces cerevisiae S288c)
Yeast vacuolar atpase a subunit (95 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunits (Complex)
V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase a subunit (67 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae S288C)

[Show more]

EMD-31539

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CryoEM Structures of Reconstituted V-ATPase,State2

Release date: Dec. 22, 2021
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7fdb
Q-score: 0.043

Khan MM, Lee S, Oot RA, Couoh-Cardel S, Kim H, Wilkens S, Roh SH

EMBO J (2021) [ ]

Sample:

V-type proton atpase subunit c (44 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit b (57 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase in rotary state 2 (1 MDa, Complex from Saccharomyces cerevisiae S288c)
Chimeric subunit h (Complex from Saccharomyces cerevisiae S288c)
Yeast vacuolar atpase f subunit (9 kDa, Protein from Saccharomyces cerevisiae S288C)
Fusion of yeast v-type proton atpase subunit h(nt) and human v-type proton atpase subunit h(ct) (53 kDa, Protein from Homo sapiens)
V-type proton atpase subunit d (29 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit g (13 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase c subunit (Complex from Saccharomyces cerevisiae S288c)
V-type proton atpase subunit e (26 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase a subunit (95 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunits (Complex)
V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase a subunit (67 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae S288C)

[Show more]

EMD-31540

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CryoEM Structures of Reconstituted V-ATPase, state3

Release date: Dec. 22, 2021
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 7fdc
Q-score: 0.069

Khan MM, Lee S, Oot RA, Couoh-Cardel S, Kim H, Wilkens S, Roh SH

EMBO J (2021) [ ]

Sample:

V-type proton atpase subunit c (44 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit b (57 kDa, Protein from Saccharomyces cerevisiae S288C)
Chimeric subunit h (Complex from Saccharomyces cerevisiae S288c)
Yeast vacuolar atpase f subunit (9 kDa, Protein from Saccharomyces cerevisiae S288C)
Fusion of yeast v-type proton atpase subunit h(nt) and human v-type proton atpase subunit h(ct) (53 kDa, Protein from Homo sapiens)
V-type proton atpase subunit d (29 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit g (13 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase c subunit (Complex from Saccharomyces cerevisiae S288c)
V-type proton atpase subunit e (26 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase a subunit (95 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase in rotary state 3 (1 MDa, Complex from Saccharomyces cerevisiae S288c)
V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunits (Complex)
V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast vacuolar atpase a subunit (67 kDa, Protein from Saccharomyces cerevisiae S288C)
V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae S288C)

[Show more]

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Select database:

EMDB [6]

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

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