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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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author:"Forster F" AND database:"EMDB" AND author_name:"G" AND xref_links:"drugbank"

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EMD-11812

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Structure of the SARS-CoV-2 spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment

Release date: May 19, 2021
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7akd
Q-score: 0.413

Fedry J, Hurdiss DL, Wang C, Li W, Obal G, Drulyte I, Du W, Howes SC, van Kuppeveld FJM, Forster F, Bosch BJ

Sci Adv (2021) 7 [ DOI: doi:10.1126/sciadv.abf5632 Pubmed: 33958322 ]

Sample:

Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Alpha-d-mannopyranose (180 Da, Ligand)
Alpha-l-fucopyranose (164 Da, Ligand)
47d11 neutralizing antibody light chain (11 kDa, Protein from Homo sapiens)
47d11 neutralizing antibody heavy chain (13 kDa, Protein from Homo sapiens)
Complex of the sars-cov-2 spike glycoprotein with the 47d11 neutralizing antibody fab fragment (550 kDa, Complex from Homo sapiens)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

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EMD-3534

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26S proteasome in presence of ATP (s1)

Release date: March 8, 2017
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 5mp9, 5mpd
Q-score: 0.2815

Wehmer M, Rudack T, Beck F, Aufderheide A, Pfeifer G, Plitzko JM, Forster F, Schulten K, Baumeister W, Sakata E

PNAS (2017) 114 pp. 1305-1310 [ Pubmed: 28115689 DOI: doi:10.1073/pnas.1621129114 ]

Sample:

Proteasome subunit alpha type-1 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-7 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 7 homolog (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Adenosine-5'-diphosphate (427 Da, Ligand)
Proteasome subunit beta type-2 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-3 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 8 homolog (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 4 homolog (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Magnesium ion (24 Da, Ligand)
26s protease regulatory subunit 6a (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-5 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome of saccharomyces cerevisiae in presence of atp (s1) (1 MDa, Complex from Saccharomyces cerevisiae S288c)
Proteasome subunit alpha type-2 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-1 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-4 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Probable proteasome subunit alpha type-7 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-6 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-5 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-6 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Adenosine-5'-triphosphate (507 Da, Ligand)
Proteasome subunit beta type-4 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease subunit rpt4 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-3 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 6b homolog (47 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-3535

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26S proteasome in presence of ATP (s2)

Release date: March 8, 2017
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 5mpa, 5mpe
Q-score: 0.2305

Wehmer M, Rudack T, Beck F, Aufderheide A, Pfeifer G, Plitzko JM, Forster F, Schulten K, Baumeister W, Sakata E

PNAS (2017) 114 pp. 1305-1310 [ Pubmed: 28115689 DOI: doi:10.1073/pnas.1621129114 ]

Sample:

Proteasome subunit alpha type-1 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-7 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 7 homolog (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Adenosine-5'-diphosphate (427 Da, Ligand)
Proteasome subunit beta type-2 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-3 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 8 homolog (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 4 homolog (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Magnesium ion (24 Da, Ligand)
26s protease regulatory subunit 6a (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome of saccharomyces cerevisiae in presence of atp (s2) (1 MDa, Complex from Saccharomyces cerevisiae S288c)
Proteasome subunit alpha type-5 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-2 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-1 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-4 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Probable proteasome subunit alpha type-7 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-6 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-5 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-6 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Adenosine-5'-triphosphate (507 Da, Ligand)
Proteasome subunit beta type-4 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease subunit rpt4 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-3 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 6b homolog (47 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-3536

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26S proteasome in presence of AMP-PNP (s3)

Release date: March 8, 2017
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 5mpb
Q-score: 0.132

Wehmer M, Rudack T, Beck F, Aufderheide A, Pfeifer G, Plitzko JM, Forster F, Schulten K, Baumeister W, Sakata E

PNAS (2017) 114 pp. 1305-1310 [ Pubmed: 28115689 DOI: doi:10.1073/pnas.1621129114 ]

Sample:

Proteasome subunit alpha type-1 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn12 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-7 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 7 homolog (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Adenosine-5'-diphosphate (427 Da, Ligand)
Proteasome subunit beta type-2 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn8 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-3 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 8 homolog (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Ubiquitin carboxyl-terminal hydrolase rpn11 (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn5 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 4 homolog (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn10 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Magnesium ion (24 Da, Ligand)
26s proteasome regulatory subunit rpn13 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 6a (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome complex subunit sem1 (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-5 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn2 (104 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome of saccharomyces cerevisiae in presence of amp-pnp (1 MDa, Complex from Saccharomyces cerevisiae S288c)
Proteasome subunit alpha type-2 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-1 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-4 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn9 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Probable proteasome subunit alpha type-7 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn6 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn1 (109 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-6 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-5 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-6 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
Proteasome subunit beta type-4 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease subunit rpt4 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-3 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn3 (60 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 6b homolog (47 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-3537

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26S proteasome in presence of BeFx (s4)

Release date: March 8, 2017
Resolution: 7.7 Å
EM Method: Single-particle
Fitted PDBs: 5mpc
Q-score: 0.135

Wehmer M, Rudack T, Beck F, Aufderheide A, Pfeifer G, Plitzko JM, Forster F, Schulten K, Baumeister W, Sakata E

PNAS (2017) 114 pp. 1305-1310 [ Pubmed: 28115689 DOI: doi:10.1073/pnas.1621129114 ]

Sample:

Proteasome subunit alpha type-1 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn12 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-7 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 7 homolog (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Adenosine-5'-diphosphate (427 Da, Ligand)
Proteasome subunit beta type-2 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn8 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-3 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 8 homolog (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Ubiquitin carboxyl-terminal hydrolase rpn11 (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn5 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 4 homolog (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn10 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Magnesium ion (24 Da, Ligand)
26s proteasome regulatory subunit rpn13 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 6a (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome of saccharomyces cerevisiae in presence of befx (s4) (1 MDa, Complex from Saccharomyces cerevisiae S288c)
26s proteasome complex subunit sem1 (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-5 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn2 (104 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-2 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Ubiquitin carboxyl-terminal hydrolase 6 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-1 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-4 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn9 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Probable proteasome subunit alpha type-7 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn6 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn1 (109 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-6 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit beta type-5 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-6 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Adenosine-5'-triphosphate (507 Da, Ligand)
Proteasome subunit beta type-4 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease subunit rpt4 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Proteasome subunit alpha type-3 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s proteasome regulatory subunit rpn3 (60 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
26s protease regulatory subunit 6b homolog (47 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

[Show more]

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EMDB [5]

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