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Yorodumi- EMDB-17629: Symmetry expanded D7 local refined map of mitochondrial heat-shoc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17629 | |||||||||
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Title | Symmetry expanded D7 local refined map of mitochondrial heat-shock protein 60-like protein from Chaetomium thermophilum | |||||||||
Map data | ||||||||||
Sample |
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Keywords | mitochondrial heat-shock protein 60-like protein / Stress response / ATP-binding / Nucleotide-binding / Chaetomium thermophilum / native cell extracts / CHAPERONE | |||||||||
Function / homology | Function and homology information ATP-dependent protein folding chaperone / protein refolding / ATP binding Similarity search - Function | |||||||||
Biological species | Thermochaetoides thermophila (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Semchonok DA / Kyrilis FL / Hamdi F / Kastritis PL | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Symmetry expanded D7, locally refined cryo-EM map of mitochondrial heat shock protein 60-like protein Chaetomium thermophilum. Authors: Semchonok DA / Kyrilis FL / Hamdi F / Kastritis PL | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17629.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-17629-v30.xml emd-17629.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17629_fsc.xml | 8.8 KB | Display | FSC data file |
Images | emd_17629.png | 84.1 KB | ||
Masks | emd_17629_msk_1.map | 64 MB | Mask map | |
Others | emd_17629_half_map_1.map.gz emd_17629_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17629 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17629 | HTTPS FTP |
-Validation report
Summary document | emd_17629_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17629_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17629_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_17629_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17629 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17629 | HTTPS FTP |
-Related structure data
Related structure data | 8pe8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17629.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.96 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17629_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17629_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17629_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : native cell extract of Chaetomium thermophilum
Entire | Name: native cell extract of Chaetomium thermophilum |
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Components |
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-Supramolecule #1: native cell extract of Chaetomium thermophilum
Supramolecule | Name: native cell extract of Chaetomium thermophilum / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: Purified and fractionated (fraction 25) cell lysate of Chaetomium thermophilum |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Molecular weight | Theoretical: 60 KDa |
-Macromolecule #1: Mitochondrial heat shock protein 60-like protein
Macromolecule | Name: Mitochondrial heat shock protein 60-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Molecular weight | Theoretical: 60.669473 KDa |
Sequence | String: MQRALTRASV SSPLATARVR SAQQLRFAHK ELKFGVEGRA ALLNGVETLA KAVATTLGPK GRNVLIESTF GSPKITKDGV TVAKAISLK DKFENLGAKL LAEVASKTNE VAGDGTTTAT VLARAIFSEM VKNVAAGCNP MDLRRGIQAA VDAVVEYLQQ N KRDITTSA ...String: MQRALTRASV SSPLATARVR SAQQLRFAHK ELKFGVEGRA ALLNGVETLA KAVATTLGPK GRNVLIESTF GSPKITKDGV TVAKAISLK DKFENLGAKL LAEVASKTNE VAGDGTTTAT VLARAIFSEM VKNVAAGCNP MDLRRGIQAA VDAVVEYLQQ N KRDITTSA EIAQVATISA NGDQHIGKLI ASAMEKVGKE GVITVKEGKT LQDELEVTEG MRFDRGFVSP YFITDAKAQK VE FEKPLIL LSEQKISAAT DIIPALEISH KMRRPLVIIA EDIDGEALAV CILNKLRGQL EVAAVKAPGF GDNRKSILGD IAV LTNGTV FTNELDVKLE KVTPDMLGST GSITITKEDT IILNGDGSKD AIAQRCEQIR GAMNDPSTSE YEKEKLQERL AKLS GGVAV IKVGGSSEVE VGEKKDRFVD ALNATRAAVE EGILPGGGTA LIKASVNALN NLKPANFDQQ LGVNIIKNAI TRPAR MIVE NAGLEGSVVI GKISDEYAAD FNKGFNSATG EYVDMIQAGI LDPLKVVRTG LIDASGVASL LGTTEVAIVE APEEKG PAG GMGGMGGMGG MM UniProtKB: Mitochondrial heat shock protein 60-like protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Specialist optics | Phase plate: OTHER |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1109 / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model Details: The initial model consisted of the complete monomeric unit of HSP60 |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-8pe8: |