The EMPIAR-PDBj team at Osaka University assists Asian EM researchers with the transfer of big EM image data to EMPIAR. Instead of sending the data directly to the EBI (UK) via the internet, hard drives can also be sent to Osaka University by postal mail or via a courier service. As an alternative, internet transfer to our server in Osaka is also available. If you would like to take advantage of our submission services, please contact us first by e-mail before sending the data to us.
We have seen a large number of SARS-CoV-2 structures being determined rapidly and deposited into the PDB and EMDB, which provides a starting point for structure-guided drug discovery. In order to validate and reanalyze the data by the cryo-EM community, we would like to make the following urgent appeal. a) If you have deposited any cryo-EM structures related to SARS-CoV-2 to the EMDB (and possibly the PDB), please deposit the raw data to EMPIAR. b) If you have collected cryo-EM data related to SARS-CoV-2 but have not yet deposited a structure, please consider depositing the raw data to EMPIAR, so that the cryo-EM community could contribute to processing and model-building.
Release date | Imageset | Title | Authors and references | Size | Resolution |
---|---|---|---|---|---|
2022-04-29 | Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA [multiple data sets in TIFF format] | Baudin F, Murciano B, Fung HKH, Fromm SA, Mattei S, Mahamid J, Müller CW [Pubmed: 35442737] [DOI: 10.1126/sciadv.abn5725] |
3.1 TB | 2.8 Å | |
2018-02-08 | Tilt-series of salmonella enterica wild-type bacterial flagellar motor [1 tilt series in MRC format] | Beeby M, Ribardo DA, Brennan CA, Ruby EG, Jensen GJ, Hendrixson DR [Pubmed: 26976588] [DOI: 10.1073/pnas.1518952113] |
328.0 MB | 69.4 Å | |
2024-02-15 | FIB-SEM dataset showing localization of a Golgi matrix protein GM130 in human hepatocellular carcinoma cell (Huh-7) [564 reconstructed volumes in TIFF format] | Belevich I, Jokitalo E | 1.1 GB | — | |
2024-01-16 | REEP3 and REEP4 determine the tubular morphology of the endoplasmic reticulum during mitosis [multiple data sets in DM4 and TIFF formats] | Belevich I, Jokitalo E [Pubmed: 30995177] [DOI: 10.1091/mbc.e18-11-0698] |
8.7 GB | — | |
2024-02-15 | FIB-SEM dataset of a human bone osteosarcoma epithelial cell (U2-OS) [1168 micrographs in TIFF format] | Belevich I, Schertel A, Zaversek T, Szyrynska N, Saarnio S, Jokitalo E | 5.2 GB | — | |
2023-01-30 | Structure of RecT protein from Listeria innoccua phage A118 in complex with 83-mer annealed duplex [2038 multi-frame micrographs composed of 36 frames each in MRC format] | Bell CE [Pubmed: 36543802] [DOI: 10.1038/s41467-022-35572-z] |
1.6 TB | 3.4 Å | |
2023-01-16 | Structure of RecT protein from Listeria innoccua phage A118 in complex with 83-mer single stranded DNA [1619 multi-frame micrographs composed of 45 frames each in TIFF format] | Bell CE [Pubmed: 36543802] [DOI: 10.1038/s41467-022-35572-z] |
822.3 GB | 4.5 Å | |
2022-07-12 | C2-symmetric single-particle cryo-EM map of T. vaginalis FDPF3 - unaligned multi-frame micrographs [stack of 7398 particles in TIFF format] | Bell TA [Pubmed: 35780837] [DOI: 10.1016/j.jbc.2022.102210] |
1.4 TB | 6.6 - 6.8 Å | |
2021-06-11 | Single particle cryo EM dataset of SARS-CoV-2 Spike protein with D614G substitution [10051 multi-frame micrographs composed of 32 frames each in MRC format] | Benton DJ, Wrobel AG, Rosenthal PB, Gamblin SJ [Pubmed: 33579792] [DOI: 10.1073/pnas.2022586118] |
4.5 TB | 3.5 - 4.2 Å | |
2020-11-27 | Micrograph frames from 110 internal SEMC/NYSBC test datasets used for Topaz-Denoise model generation & analysis [1000000 micrographs in MRCS format] | Bepler T, Kelley K, Noble AJ, Berger B [Pubmed: 33060581] [DOI: 10.1038/s41467-020-18952-1] |
33.9 TB | 2.9 - 12.54 Å | |
2019-04-05 | Rabbit muscle aldolase single particle cryoEM [multiple data sets in MRC format] | Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble AJ, Berger B [Pubmed: 31591578] [DOI: 10.1038/s41592-019-0575-8] |
1.4 TB | 3.7 - 3.92 Å | |
2022-03-01 | Helical structure of the toxin MakA from Vibrio cholera [1351 multi-frame micrographs composed of 40 frames each in TIFF format] | Berg A, Nadeem A, Uhlin BE, Wai SN, Barandun J [Pubmed: 35131030] [DOI: 10.7554/eLife.73439] |
195.8 GB | 3.65 Å | |
2023-02-03 | Cryo-electron tomography on plasma FIB lamellae of HeLa cells [6481 tilt series in EER format] | Berger C, Dumoux M, Glen T, Yee NB, Mitchels JM, Patáková Z, Darrow MC, Naismith JH, Grange M [Pubmed: 36746945] [DOI: 10.1038/s41467-023-36372-9] |
622.2 GB | 4.9 Å | |
2015-11-19 | Sub-tomogram averaging in RELION [7 class averages in MRC format] | Bharat TA, Scheres SH [Pubmed: 27685097] [DOI: 10.1038/nprot.2016.124] |
842.8 GB | 13.0 Å | |
2018-05-02 | Correlative microscopy of vitreous sections provides insights into BAR-domain organisation in situ [9 tilt series in MRC format] | Bharat TAM, Hoffmann PC, Kukulski W [Pubmed: 29681471] [DOI: 10.1016/j.str.2018.03.015] |
27.9 GB | — | |
2020-08-25 | Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation [stack of 6649 particles in MRC format] | Bhargava K, Datta PP, Kaushal PS, Keshavan P, Spremulli LL, Banavali NK [Pubmed: 32737313] [DOI: 10.1038/s41467-020-17715-2] |
753.5 GB | 2.96 - 3.96 Å | |
2023-02-13 | Tobacco mosaic virus, imaged on a JEOL CRYOARM 300 and Direct Electron Apollo [3402 multi-frame micrographs composed of 45 frames each in TIFF format] | Bhella D, Love AJ, Streetley J, Taliansky M, McGeachy K, Bukharova T | 1.1 TB | 1.85 Å | |
2020-04-09 | Cryo-EM structure of Lumazine Synthase [1198 multi-frame micrographs composed of 41 frames each in MRC format] | Bhella D, Streetley J, Clarke M, Cowton V, Patel A [Pubmed: 31359340] [DOI: 10.1007/s12551-019-00571-w] |
3.0 TB | 2.0 Å | |
2020-04-09 | Cryo-EM structure of Lumazine Synthase [2874 multi-frame micrographs composed of 39 frames each in MRC format] | Bhella D, Streetley J, Clarke M, Cowton V, Patel A [Pubmed: 31359340] [DOI: 10.1007/s12551-019-00571-w] |
6.8 TB | 2.0 Å | |
2022-09-26 | In situ cryo-electron tomography of autophagic structures in S. cerevisiae [84 tilt series in MRC format] | Bieber A, Capitanio C, Erdmann PS, Schulman BA, Baumeister W, Wilfling F [Pubmed: 36122245] [DOI: 10.1073/pnas.2209823119] |
249.0 GB | — | |
2023-10-03 | Single particle cryo-EM dataset of bovine complex I in the deactive state [2988 multi-frame micrographs composed of 20 frames each in MRC format] | Blaza JN, Vinothkumar KR, Hirst J [Pubmed: 29395787] [DOI: 10.1016/j.str.2017.12.014] |
965.8 GB | 4.13 Å | |
2020-07-14 | 3 Å resolution single particle reconstruction of glucosyltransferase ALG6 in nanodisc [multiple data sets in MRC and TIFF formats] | Bloch JS, Pesciullesi G, Boilevin J, Nosol K, Irobalieva RN, Darbre T, Aebi M, Kossiakoff AA, Reymond JL, Locher KP [Pubmed: 32103179] [DOI: 10.1038/s41586-020-2044-z] |
2.8 TB | 3.0 Å | |
2023-10-10 | EM ladder: four-species cryoEM protein mix for workflow and algorithm benchmarking: Apoferritin, beta-galactosidase, PP7 VLPs and TMV [1862 micrographs in MRC format] | Bobe D, Eng E, Kopylov M | 98.7 GB | 2.38 - 3.36 Å | |
2023-10-13 | Single-particle cryo-EM of APC/C-CDH1-UBE2C-UBE2S-Ubiquitin-CyclinB-NTD [25837 multi-frame micrographs composed of 39 frames each in TIFF format] | Bodrug T, Welsh KA, Bolhuis DL, Paulаkonis E, Martinez-Chacin RC, Liu B, Pinkin N, Bonacci T, Cui L, Xu P, Roscow O, Amann SJ, Grishkovskaya I, Emanuele MJ, Harrison JS, Steimel JP, Hahn KM, Zhang W, Zhong ED, Haselbach D, Brown NG [Pubmed: 37735619] [DOI: 10.1038/s41594-023-01105-5] |
22.8 TB | 3.5 Å | |
2023-10-03 | Single-particle cryo-EM of APC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD [25354 multi-frame micrographs composed of 39 frames each in TIFF format] | Bodrug T, Welsh KA, Bolhuis DL, Paulаkonis E, Martinez-Chacin RC, Liu B, Pinkin N, Bonacci T, Cui L, Xu P, Roscow O, Amann SJ, Grishkovskaya I, Emanuele MJ, Harrison JS, Steimel JP, Hahn KM, Zhang W, Zhong ED, Haselbach D, Brown NG [Pubmed: 37735619] [DOI: 10.1038/s41594-023-01105-5] |
19.0 TB | 4.0 Å |