+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-61187 | |||||||||
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Title | T.acidophilum 20S proteasome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Protein degradation / Ubiquitin Proteasome System / CYTOSOLIC PROTEIN | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Shao X / Tian M | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Biofunctionalized dissolvable hydrogel microbeads enable efficient characterization of native protein complexes Authors: Shao X / Tian M / Wang G / Wang J / Wang H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_61187.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-61187-v30.xml emd-61187.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_61187_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_61187.png | 101.5 KB | ||
Masks | emd_61187_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-61187.cif.gz | 5.1 KB | ||
Others | emd_61187_half_map_1.map.gz emd_61187_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-61187 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-61187 | HTTPS FTP |
-Validation report
Summary document | emd_61187_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_61187_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_61187_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_61187_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61187 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61187 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_61187.map.gz / Format: CCP4 / Size: 103 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: 0.94 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_61187_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_61187_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_61187_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 28mer protein molecular machine composed of 14 alpha subunits and...
Entire | Name: 28mer protein molecular machine composed of 14 alpha subunits and 14 beta subunits |
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Components |
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-Supramolecule #1: 28mer protein molecular machine composed of 14 alpha subunits and...
Supramolecule | Name: 28mer protein molecular machine composed of 14 alpha subunits and 14 beta subunits type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 690 KDa |
-Macromolecule #1: T.acidophilum 20S proteasome
Macromolecule | Name: T.acidophilum 20S proteasome / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Recombinant expression | Organism: Escherichia (bacteria) |
Sequence | String: MGMQQGQMAY DRAITVFSPD GRLFQVEYAR EAVKKGSTAL GMKFANGVLL ISDKKVRSRL IEQNSIEKIQ LIDDYVAAVT SGLVADARVL VDFARISAQQ EKVTYGSLVN IENLVKRVAD QMQQYTQYGG VRPYGVSLIF AGIDQIGPRL FDCDPAGTIN EYKATAIGSG ...String: MGMQQGQMAY DRAITVFSPD GRLFQVEYAR EAVKKGSTAL GMKFANGVLL ISDKKVRSRL IEQNSIEKIQ LIDDYVAAVT SGLVADARVL VDFARISAQQ EKVTYGSLVN IENLVKRVAD QMQQYTQYGG VRPYGVSLIF AGIDQIGPRL FDCDPAGTIN EYKATAIGSG KDAVVSFLER EYKENLPEKE AVTLGIKALK SSLEEGEELK APEIASITVG NKYRIYDQEE VKKFLMNQTL ETGTTTVGIT LKDAVIMATE RRVTMENFIM HKNGKKLFQI DTYTGMTIAG LVGDAQVLVR YMKAELELYR LQRRVNMPIE AVATLLSNML NQVKYMPYMV QLLVGGIDTA PHVFSIDAAG GSVEDIYAST GSGSPFVYGV LESQYSEKMT VDEGVDLVIR AISAAKQRDS ASGGMIDVAV ITRKDGYVQL PTDQIESRIR KLGLILHHHH HH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.2 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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