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Protocols

EMPIAR specifications

Information


Unique identifier OMICS_11376
Name EMPIAR
Alternative name Electron Microscopy Pilot Image Archive
Restrictions to use None
Community driven Yes
Data access File download, Browse
User data submission Allowed
Maintained Yes

Publication for Electron Microscopy Pilot Image Archive

EMPIAR citations

 (12)
library_books

Cryo EM structure of the protein conducting ERAD channel Hrd1 in complex with Hrd3

2017
Nature
PMCID: 5736104
PMID: 28682307
DOI: 10.1038/nature23314

[…] ively. The cryo-EM maps of the Hrd1/Hrd3 complexes containing one or two Hrd3 molecules were deposited with accession codes EMD-8639 and EMD-8638, respectively. The raw cryo-EM data were deposited to EMPIAR (accession code EMPIAR-10099). An interactive session of models with co-evolution data can be found at http://gremlin.bakerlab.org/hrd. […]

library_books

Helical reconstruction in RELION

2017
J Struct Biol
PMCID: 5479445
PMID: 28193500
DOI: 10.1016/j.jsb.2017.02.003

[…] our MamK data set, and particle polishing was performed when we initially published this data set (), we chose not to re-process the movie frames of this large data set for this paper. The VipA/VipB EMPIAR entry does not contain movies, so no movie processing was performed.After 3D auto-refinement of the polished particles, we attempted further selection of the best segments by 3D classification. […]

library_books

High resolution Single Particle Analysis from Electron Cryo microscopy Images Using SPHIRE

2017
PMCID: 5607996
PMID: 28570515
DOI: 10.3791/55448

[…] for the understanding of complex molecular mechanisms. ACCESION CODES: The coordinates for the EM structure and the unprocessed movies have been deposited in the Electron Microscopy Data Bank and the Electron Microscopy Pilot Image Archive under accession numbers EMD-3645 and EMPIAR-10089, respectively. […]

library_books

A pipeline approach to single particle processing in RELION

2017
Acta Crystallogr D Struct Biol
PMCID: 5458491
PMID: 28580911
DOI: 10.1107/S2059798316019276

[…] To demonstrate the new pipeline, we reprocessed a data set from the EMPIAR database (Iudin et al., 2016): entry 10028 (Wong et al., 2014). This cryo-EM data set comprises 1081 16-frame movies of 4096 × 4096 pixels that were collected using a Falcon-II direct-electron […]

library_books

Building bridges between cellular and molecular structural biology

2017
eLife
PMCID: 5524535
PMID: 28682240
DOI: 10.7554/eLife.25835.008

[…] structured biological annotation to segmentations obtained from a variety of different software packages and then output an annotated segmentation file in EMDB-SFF that could be deposited to EMDB or EMPIAR. Annotation could either be done during deposition, in which case the biological annotation from the segmentation file could be harvested by the deposition system to facilitate the deposition p […]

call_split

Using the Volta phase plate with defocus for cryo EM single particle analysis

2017
eLife
PMCID: 5279940
PMID: 28109158
DOI: 10.7554/eLife.23006.013
call_split See protocol

[…] from the Relion particle polishing and MotionCor2 data processing workflows were deposited to the EMDataBank with accession codes EMD-3455 and EMD-3456 respectively. The dataset was deposited to the Electron Microscopy Pilot Image Archive with accession code EMPIAR-10078. […]

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EMPIAR institution(s)
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
EMPIAR funding source(s)
This work was supported by the UK Medical Research Council with cofunding from the UK Biotechnology and Biological Sciences Research Council (BBSRC; grant MR/L007835) and by the BBSRC (grant BB/M018423/1). Work on EMDB at PDBe is supported by the Wellcome Trust (grants 088944 and 104948), the European Commission Framework 7 Programme (grant 284209), the US National Institutes of Health National Institute of General Medical Sciences (grant R01 GM079429) and EMBL-EBI.

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