Electron Microscopy Data Bank

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Subtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes

Release date: Aug. 14, 2024
Resolution: 4.1 Å
EM Method: Subtomogram averaging
Fitted PDBs: 8tpu

Anton L, Cheng W, Haile M, Cobb DW, Zhu X, Han L, Li E, Nair A, Lee CL, Ho CM

To Be Published

Sample:

40s ribosomal protein s7 (22 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s27 (9 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s19 (16 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l29 (8 kDa, Protein from Plasmodium falciparum 3D7)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s5, putative (21 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l27 (16 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l17, putative (19 kDa, Protein from Plasmodium falciparum 3D7)
Large ribosomal subunit protein el43 (10 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s3a (30 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l7a (32 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s10, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l27a, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s23, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s15a, putative (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l4 (46 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l41 (6 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l34 (17 kDa, Protein from Plasmodium falciparum 3D7)
5.8s ribosomal rna (51 kDa, RNA from Plasmodium falciparum 3D7)
60s ribosomal protein l30e, putative (11 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l5, putative (34 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l39 (6 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s24 (15 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l3 (44 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s5 (30 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l7, putative (30 kDa, Protein from Plasmodium falciparum 3D7)
Small ribosomal subunit protein es30 (4 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l18a (21 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l24, putative (19 kDa, Protein from Plasmodium falciparum 3D7)
Ribosomal protein l15 (23 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l14, putative (19 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l6, putative (25 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l19 (21 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s17, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s4 (29 kDa, Protein from Plasmodium falciparum 3D7)
18s ribosomal rna (669 kDa, RNA from Plasmodium falciparum 3D7)
40s ribosomal protein s6 (35 kDa, Protein from Plasmodium falciparum 3D7)
Receptor for activated c kinase (35 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l21 (18 kDa, Protein from Plasmodium falciparum 3D7)
Plasmodium falciparum 80s ribosome consensus structure (Complex from Plasmodium falciparum 3D7)
60s ribosomal protein l23 (22 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s3 (24 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s20e, putative (13 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s25 (11 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l6, putative (21 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l41 (5 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s19 (19 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s9, putative (22 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l31 (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l23, putative (15 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l2 (28 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l22, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s21 (9 kDa, Protein from Plasmodium falciparum 3D7)
5s ribosomal rna (38 kDa, RNA from Plasmodium falciparum 3D7)
60s ribosomal protein l13 (25 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l28 (14 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l24, putative (23 kDa, RNA from Plasmodium falciparum 3D7)
40s ribosomal protein s29, putative (6 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s15 (17 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l10, putative (25 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l32 (15 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s16 (16 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s11 (16 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s11, putative (18 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s18, putative (17 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s8 (25 kDa, Protein from Plasmodium falciparum 3D7)
Ribosomal protein l37 (10 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l38 (10 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l18-2, putative (21 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l26, putative (14 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein sa (29 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l11a, putative (20 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l35ae, putative (16 kDa, Protein from Plasmodium falciparum 3D7)
Large ribosomal subunit protein el42 (12 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l35, putative (14 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s26 (12 kDa, Protein from Plasmodium falciparum 3D7)
28s ribosomal rna (1 MDa, RNA from Plasmodium falciparum 3D7)
60s ribosomal protein l36 (12 kDa, Protein from Plasmodium falciparum 3D7)
40s ribosomal protein s12 (15 kDa, Protein from Plasmodium falciparum 3D7)
60s ribosomal protein l13, putative (23 kDa, Protein from Plasmodium falciparum 3D7)

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EMD-19276

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Cryo-EM of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C1)

Release date: March 13, 2024
Resolution: 4.6 Å
EM Method: Single-particle

Nishio S, Emori C, Wiseman B, Fahrenkamp D, Dioguardi E, Zamora-Caballero S, Bokhove M, Han L, Stsiapanava A, Algarra B, Lu Y, Kodani M, Bainbridge RE, Komondor KM, Carlson AE, Landreh M, de Sanctis D, Yasumasu S, Ikawa M, Jovine L

Cell (2024) 187 pp. 1440-1459.e24 [ DOI: doi:10.1016/j.cell.2024.02.013 Pubmed: 38490181 ]

Sample:

EMD-19277

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Cryo-EM of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C2)

Release date: March 13, 2024
Resolution: 4.4 Å
EM Method: Single-particle

Cell (2024) 187 pp. 1440-1459.e24 [ DOI: doi:10.1016/j.cell.2024.02.013 Pubmed: 38490181 ]

Sample:

EMD-24265

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E. coli cytochrome bo3 in MSP nanodisc

Release date: Sept. 1, 2021
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 7n9z
Q-score: 0.734

Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R

PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]

Sample:

Zinc ion (65 Da, Ligand)
Cytochrome o ubiquinol oxidase (22 kDa, Protein from Escherichia coli)
Ubiquinone-8 (727 Da, Ligand)
Cytochrome o ubiquinol oxidase, subunit i (74 kDa, Protein from Escherichia coli)
1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
Cytochrome o ubiquinol oxidase, subunit iv (12 kDa, Protein from Escherichia coli)
Heme o (838 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Cytochrome bo 3 ubiquinol oxidase (Complex from Escherichia coli)
Ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Copper (ii) ion (63 Da, Ligand)
Cardiolipin (1 kDa, Ligand)
Water (18 Da, Ligand)

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EMD-30471

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2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane

Release date: Aug. 25, 2021
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 7cub
Q-score: 0.645

Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R

PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]

Sample:

1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
Ubiquinone-8 (727 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
Heme o (838 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
Copper (ii) ion (63 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)

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EMD-30474

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2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane

Release date: Aug. 25, 2021
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 7cuq
Q-score: 0.597

Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R

PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]

Sample:

1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
Ubiquinone-8 (727 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
Heme o (838 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
Copper (ii) ion (63 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)

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EMD-30475

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Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli

Release date: Aug. 25, 2021
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 7cuw
Q-score: 0.63

Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R

PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]

Sample:

1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
Ubiquinone-8 (727 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
Heme o (838 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
Copper (ii) ion (63 Da, Ligand)
Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)

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