Electron Microscopy Data Bank

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The structure of the Plasmodium falciparum 20S proteasome in complex with two PA28 activators.

Release date: Aug. 7, 2019
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6muv
Q-score: 0.397

Xie SC, Metcalfe RD, Hanssen E, Yang T, Gillett DL, Leis AP, Morton CJ, Kuiper MJ, Parker MW, Spillman NJ, Wong W, Tsu C, Dick LR, Griffin MDW, Tilley L

Nat Microbiol (2019) 4 pp. 1990-2000 [ Pubmed: 31384003 DOI: doi:10.1038/s41564-019-0524-4 ]

Sample:

20s proteasome alpha-5 subunit (28 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-1 subunit (29 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-3 subunit (27 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-4 subunit (27 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-4 subunit (22 kDa, Protein from Plasmodium falciparum (isolate 3D7))
Proteasome activator pa28 (33 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-2 subunit (25 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-3 subunit (24 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-7 subunit (30 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-5 subunit (23 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-6 subunit (27 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-7 subunit (29 kDa, Protein from Plasmodium falciparum (isolate 3D7))
11s activator of the plasmodium falciparum proteasome. (Complex from Plasmodium falciparum 3D7)
20s proteasome/pa28 complex. (230 kDa, Complex from Plasmodium falciparum 3D7)
20s proteasome beta-1 subunit (29 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-2 subunit (26 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-6 subunit (28 kDa, Protein from Plasmodium falciparum (isolate 3D7))
Plasmodium falciparum 20s proteasome (Complex from Plasmodium falciparum 3D7)

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EMD-9258

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The structure of the Plasmodium falciparum 20S proteasome.

Release date: Aug. 7, 2019
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6muw
Q-score: 0.461

Xie SC, Metcalfe RD, Hanssen E, Yang T, Gillett DL, Leis AP, Morton CJ, Kuiper MJ, Parker MW, Spillman NJ, Wong W, Tsu C, Dick LR, Griffin MDW, Tilley L

Nat Microbiol (2019) 4 pp. 1990-2000 [ DOI: doi:10.1038/s41564-019-0524-4 Pubmed: 31384003 ]

Sample:

20s proteasome alpha-3 subunit (27 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-7 subunit (29 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-5 subunit (23 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-3 subunit (24 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-7 subunit (30 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-4 subunit (27 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-6 subunit (27 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-1 subunit (29 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-5 subunit (28 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-1 subunit (29 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-2 subunit (26 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome beta-2 subunit (25 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome/pa28 complex. (760 kDa, Complex from Plasmodium falciparum 3D7)
20s proteasome beta-4 subunit (22 kDa, Protein from Plasmodium falciparum (isolate 3D7))
20s proteasome alpha-6 subunit (28 kDa, Protein from Plasmodium falciparum (isolate 3D7))

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EMD-9259

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The structure of the Plasmodium falciparum 20S proteasome in complex with one PA28 activator.

Release date: Aug. 7, 2019
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6mux
Q-score: 0.439

Xie SC, Metcalfe RD, Hanssen E, Yang T, Gillett DL, Leis AP, Morton CJ, Kuiper MJ, Parker MW, Spillman NJ, Wong W, Tsu C, Dick LR, Griffin MDW, Tilley L

Nat Microbiol (2019) 4 pp. 1990-2000 [ Pubmed: 31384003 DOI: doi:10.1038/s41564-019-0524-4 ]

Sample:

20s proteasome alpha-7 subunit (29 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome beta-2 subunit (25 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome beta-7 subunit (30 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome alpha-1 subunit (29 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome beta-6 subunit (27 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome beta-1 subunit (29 kDa, Protein from Plasmodium falciparum 3D7)
11s activator of the plasmodium falciparum proteasome. (Complex from Plasmodium falciparum 3D7)
20s proteasome beta-4 subunit (22 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome/pa28 complex. (230 kDa, Complex from Plasmodium falciparum 3D7)
20s proteasome beta-5 subunit (23 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome alpha-3 subunit (27 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome beta-3 subunit (24 kDa, Protein from Plasmodium falciparum 3D7)
Proteasome activator pa28 (33 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome alpha-6 subunit (28 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome alpha-5 subunit (28 kDa, Protein from Plasmodium falciparum 3D7)
Plasmodium falciparum 20s proteasome (Complex from Plasmodium falciparum 3D7)
20s proteasome alpha-4 subunit (27 kDa, Protein from Plasmodium falciparum 3D7)
20s proteasome alpha-2 subunit (26 kDa, Protein from Plasmodium falciparum 3D7)

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EMD-20073

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Reconstruction of the Plasmodium falciparum 20S proteasome in complex with one PA28 activator prepared without chemical stabilisation

Release date: Aug. 7, 2019
Resolution: 4.6 Å
EM Method: Single-particle

Xie SC, Metcalfe RD, Hanssen E, Yang T, Gillett DL, Leis AP, Morton CJ, Kuiper MJ, Parker MW, Spillman NJ, Wong W, Tsu C, Dick LR, Griffin MDW, Tilley L

Nat Microbiol (2019) 4 pp. 1990-2000 [ Pubmed: 31384003 DOI: doi:10.1038/s41564-019-0524-4 ]

Sample:

11s activator of the plasmodium falciparum proteasome. (Complex from Plasmodium falciparum 3D7)
20s proteasome/pa28 complex. (230 kDa, Complex from Plasmodium falciparum 3D7)
Plasmodium falciparum 20s proteasome (Complex from Plasmodium falciparum 3D7)

EMD-9192

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Cryo-electron microscopy structure of Plasmodium falciparum Rh5/CyRPA/Ripr invasion complex

Release date: Dec. 12, 2018
Resolution: 7.17 Å
EM Method: Single-particle
Fitted PDBs: 6mpv
Q-score: 0.191

Wong W, Huang R, Menant S, Hong C, Sandow JJ, Birkinshaw RW, Healer J, Hodder AN, Kanjee U, Tonkin CJ, Heckmann D, Soroka V, Sogaard TMM, Jorgensen T, Duraisingh MT, Czabotar PE, de Jongh WA, Tham WH, Webb AI, Yu Z, Cowman AF

Nature (2019) 565 pp. 118-121 [ DOI: doi:10.1038/s41586-018-0779-6 Pubmed: 30542156 ]

Sample:

Pfripr (1 kDa, Protein from Plasmodium falciparum 3D7)
Pfripr (443 Da, Protein from Plasmodium falciparum 3D7)
Pfrh5/cyrpa/pfripr complex (Complex from Plasmodium falciparum 3D7)
Cysteine-rich protective antigen (39 kDa, Protein from Plasmodium falciparum (isolate 3D7))
Reticulocyte binding protein 5 (39 kDa, Protein from Plasmodium falciparum)

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EMD-7783

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Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; one molecule of parasite ligand.

Release date: June 20, 2018
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 6d03
Q-score: 0.482

Gruszczyk J, Huang RK, Chan LJ, Menant S, Hong C, Murphy JM, Mok YF, Griffin MDW, Pearson RD, Wong W, Cowman AF, Yu Z, Tham WH

Nature (2018) 559 pp. 135-139 [ DOI: doi:10.1038/s41586-018-0249-1 Pubmed: 29950717 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Carbonate ion (60 Da, Ligand)
Ternary complex between human transferrin receptor 1, transferrin and plasmodium vivax reticulocyte-binding protein 2b (Complex from homo sapiens)
Reticulocyte binding protein 2, putative (96 kDa, Protein from Plasmodium vivax)
Transferrin receptor protein 1 (73 kDa, Protein from Homo sapiens)
Calcium ion (40 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)
Serotransferrin (77 kDa, Protein from Human)

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EMD-7784

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Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 1.

Release date: June 20, 2018
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 6d04
Q-score: 0.444

Gruszczyk J, Huang RK, Chan LJ, Menant S, Hong C, Murphy JM, Mok YF, Griffin MDW, Pearson RD, Wong W, Cowman AF, Yu Z, Tham WH

Nature (2018) 559 pp. 135-139 [ DOI: doi:10.1038/s41586-018-0249-1 Pubmed: 29950717 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Carbonate ion (60 Da, Ligand)
Reticulocyte binding protein 2, putative (96 kDa, Protein from Plasmodium vivax)
Transferrin receptor protein 1 (73 kDa, Protein from Homo sapiens)
Calcium ion (40 Da, Ligand)
Ternary complex between human transferrin receptor 1, transferrin and plasmodium vivax reticulocyte-binding protein 2b (Complex from Homo sapiens)
Fe (iii) ion (55 Da, Ligand)
Serotransferrin (77 kDa, Protein from Human)

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EMD-7785

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Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2.

Release date: June 20, 2018
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6d05
Q-score: 0.419

Gruszczyk J, Huang RK, Chan LJ, Menant S, Hong C, Murphy JM, Mok YF, Griffin MDW, Pearson RD, Wong W, Cowman AF, Yu Z, Tham WH

Nature (2018) 559 pp. 135-139 [ Pubmed: 29950717 DOI: doi:10.1038/s41586-018-0249-1 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Carbonate ion (60 Da, Ligand)
Ternary complex between human transferrin receptor 1, transferrin and plasmodium vivax reticulocyte-binding protein 2b (Complex from homo sapiens)
Fe (iii) ion (55 Da, Ligand)
Serotransferrin (77 kDa, Protein from Human)
Reticulocyte binding protein 2, putative (96 kDa, Protein from Plasmodium vivax)
Calcium ion (40 Da, Ligand)
Transferrin receptor protein 1 (73 kDa, Protein from Homo sapiens)

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EMD-8576

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Structure of the Plasmodium falciparum 80S ribosome bound to the antimalarial drug mefloquine

Release date: March 1, 2017
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 5umd
Q-score: 0.46

Wong W, Bai XC, Sleebs BE, Triglia T, Brown A, Thompson JK, Jackson KE, Hanssen E, Marapana DS, Fernandez IS, Ralph SA, Cowman AF, Scheres SH, Baum J

Nat Microbiol (2017) 2 pp. 17031-17031 [ Pubmed: 28288098 DOI: doi:10.1038/nmicrobiol.2017.31 ]

Sample:

60s ribosomal protein l28 (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l39 (6 kDa, Protein from Plasmodium falciparum 3D7)
5.8s ribosomal rna (51 kDa, RNA from Plasmodium falciparum 3D7)
60s ribosomal protein l26, putative (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l35ae, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l37a (10 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l35, putative (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l31 (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l13 (25 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l11a, putative (20 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l18a (21 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l6-2, putative (25 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l22, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l7, putative (30 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l41 (5 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l7-3, putative (32 kDa, Protein from Plasmodium falciparum 3D7)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l19 (21 kDa, Protein from Plasmodium falciparum 3D7)
Ribosomal protein l37 (10 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l21 (18 kDa, Protein from Plasmodium falciparum 3D7)
Mefloquine (378 Da, Ligand)
60s ribosomal protein l3 (44 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l6, putative (21 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l13, putative (23 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l34 (17 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l36 (12 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l4 (46 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l27a, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l10, putative (25 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l27 (16 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l29, putative (8 kDa, Protein from Plasmodium falciparum 3D7)
Ribosomal protein l15 (24 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l18-2, putative (21 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l44 (12 kDa, Protein from Plasmodium falciparum 3D7)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l2 (28 kDa, Protein from Plasmodium falciparum 3D7)
28s ribosomal rna (1 MDa, RNA from Plasmodium falciparum 3D7)
60s ribosomal protein l5, putative (34 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l38 (10 kDa, Protein from Plasmodium falciparum 3D7)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l14, putative (19 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l17, putative (23 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l32 (15 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l23, putative (15 kDa, Protein from Plasmodium falciparum 3D7)
5s ribosomal rna (38 kDa, RNA from Plasmodium falciparum 3D7)
60s ribosomal protein l30e, putative (11 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l24, putative (19 kDa, Protein from Plasmodium falciparum 3D7)
Plasmodium falciparum 80s ribosome bound to mefloquine (4 MDa, Complex from Plasmodium falciparum 3D7)
60s ribosomal protein l23 (22 kDa, Protein from Plasmodium falciparum 3D7)

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EMPIAR-10028

Release date: June 17, 2015
Dataset size: 1.2 TB
Experiment type: EMDB

Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Scheres SH

Elife (2014) 3 [ Pubmed: 24913268 DOI: 10.7554/elife.03080 ]

Image sets:

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