Electron Microscopy Data Bank

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Structure of mutant 30S subunit with extended helix 26, version 3

Release date: Feb. 5, 2025
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 9duk
Q-score: 0.446

Boyko KV, Bernstein RA, Kim M, Cate JHD

Biochemistry (2025) 64 pp. 710-718 [ Pubmed: 39854700 DOI: doi:10.1021/acs.biochem.4c00688 ]

Sample:

30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
30s subunit (Complex from Escherichia coli)
Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
16s rrna (497 kDa, RNA from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us2 (25 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)

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EMD-47169

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Structure of mutant 30S subunit with extended helix 26, version 4

Release date: Feb. 5, 2025
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 9dul
Q-score: 0.51

Boyko KV, Bernstein RA, Kim M, Cate JHD

Biochemistry (2025) 64 pp. 710-718 [ Pubmed: 39854700 DOI: doi:10.1021/acs.biochem.4c00688 ]

Sample:

Small ribosomal subunit protein us7 (20 kDa, Protein from Escherichia coli)
30s subunit (Complex from Escherichia coli)
Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs16 (9 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us2 (25 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
16s rrna (496 kDa, RNA from Escherichia coli)
Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs6 (15 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)

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EMD-43257

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AP-6 bound human TMEM175

Release date: Aug. 14, 2024
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 8vic

Oh S, Lee J, Choi HJ, Kim S, Sapuru V, Kim M, Hite RK

J Am Chem Soc (2024) 146 pp. 23230-23239 [ Pubmed: 39116214 DOI: doi:10.1021/jacs.4c05623 ]

Sample:

(2p,2'p)-2,2'-(1,3-phenylene)di(pyridin-4-amine) (262 Da, Ligand)
Human tmem175 in an inhibitor-bound state (55 MDa, Complex from Homo sapiens)
Endosomal/lysosomal potassium channel tmem175 (55 kDa, Protein from Homo sapiens)

EMD-43259

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2-PPA bound human TMEM175

Release date: Aug. 14, 2024
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8vie

Oh S, Lee J, Choi HJ, Kim S, Sapuru V, Kim M, Hite RK

J Am Chem Soc (2024) 146 pp. 23230-23239 [ Pubmed: 39116214 DOI: doi:10.1021/jacs.4c05623 ]

Sample:

2-phenylpyridin-4-amine (170 Da, Ligand)
Human tmem175 in an inhibitor-bound state (55 MDa, Complex from Homo sapiens)
Endosomal/lysosomal potassium channel tmem175 (55 kDa, Protein from Homo sapiens)

EMD-60655

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Orf virus scaffolding protein Orfv075

Release date: Aug. 7, 2024
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 9ikc
Q-score: 0.763

Kim S, Ko S, Kim M, Jang Y, Hyun J

Biochem Biophys Res Commun (2024) 728 pp. 150334-150334 [ Pubmed: 38968773 DOI: doi:10.1016/j.bbrc.2024.150334 ]

Sample:

Orfv075 trimer (190 kDa, Complex from Orf virus (strain NZ2))
62 kda protein (63 kDa, Protein from Orf virus (strain NZ2))
Water (18 Da, Ligand)

EMPIAR-11822

Release date: June 5, 2024
Dataset size: 9.7 GB
Experiment type: EMDB

Zhu S, Bradfield CJ, Maminska A, Park ES, Kim BH, Kumar P, Huang S, Kim M, Zhang Y, Bewersdorf J, MacMicking JD

Science (2024) 383 [ Pubmed: 38422126 DOI: 10.1126/science.abm9903 ]

Image sets:

Human GBP1 on Salmonella minicell surface

EMD-43091

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hGBP1 conformer on the bacterial outer membrane

Release date: March 20, 2024
Resolution: 17.0 Å
EM Method: Subtomogram averaging

Zhu S, Bradfield CJ, Maminska A, Park ES, Kim BH, Kumar P, Huang S, Kim M, Zhang Y, Bewersdorf J, MacMicking JD

Science (2024) 383 pp. eabm9903-eabm9903 [ DOI: doi:10.1126/science.abm9903 Pubmed: 38422126 ]

Sample:

EMD-43153

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hGBP1 conformer on the bacterial outer membrane

Release date: March 20, 2024
Resolution: 9.7 Å
EM Method: Subtomogram averaging

Zhu S, Bradfield CJ, Maminska A, Park ES, Kim BH, Kumar P, Huang S, Kim M, Zhang Y, Bewersdorf J, MacMicking JD

Science (2024) 383 pp. eabm9903-eabm9903 [ DOI: doi:10.1126/science.abm9903 Pubmed: 38422126 ]

Sample:

EMD-33274

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Human Cx36/GJD2 (N-terminal deletion mutant) gap junction channel in soybean lipids (D6 symmetry)

Release date: Aug. 30, 2023
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7xl8
Q-score: 0.532

Lee SN, Cho HJ, Jeong H, Ryu B, Lee HJ, Kim M, Yoo J, Woo JS, Lee HH

Nat Commun (2023) 14 pp. 1347-1347 [ DOI: doi:10.1038/s41467-023-37040-8 Pubmed: 36906653 ]

Sample:

Cx36-deln8 (Complex from Homo sapiens)
1,2-dimyristoyl-rac-glycero-3-phosphocholine (677 Da, Ligand)
Gap junction delta-2 protein (36 kDa, Protein from Homo sapiens)

EMD-33275

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Human Cx36/GJD2 (N-terminal deletion mutant) gap junction channel in soybean lipids (C1 symmetry)

Release date: Aug. 9, 2023
Resolution: 3.41 Å
EM Method: Single-particle

Lee SN, Cho HJ, Jeong H, Ryu B, Lee HJ, Kim M, Yoo J, Woo JS, Lee HH

Nat Commun (2023) 14 pp. 1347-1347 [ DOI: doi:10.1038/s41467-023-37040-8 Pubmed: 36906653 ]

Sample:

Cx36-deln8 (Complex from Homo sapiens)

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