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Yorodumi- EMDB-21113: Cryo EM Structure of VPS13 protein, 1-1390 from C. thermophilum -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21113 | |||||||||
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Title | Cryo EM Structure of VPS13 protein, 1-1390 from C. thermophilum | |||||||||
Map data | VPS13 protein | |||||||||
Sample |
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Biological species | Chaetomium thermophilum (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Li P / Lees JA / Reinisch KM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Cell Biol / Year: 2020 Title: Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes. Authors: PeiQi Li / Joshua Aaron Lees / C Patrick Lusk / Karin M Reinisch / Abstract: A single particle cryo-EM reconstruction of an ∼160-kD N-terminal fragment of the lipid transport protein VPS13 reveals an ∼160-Å long channel lined with hydrophobic residues suitable for ...A single particle cryo-EM reconstruction of an ∼160-kD N-terminal fragment of the lipid transport protein VPS13 reveals an ∼160-Å long channel lined with hydrophobic residues suitable for solubilizing multiple lipid fatty acid moieties. The structure suggests that VPS13 and related proteins, like the autophagy protein ATG2, can act as bridges between organelle membranes to allow bulk lipid flow between organelles. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21113.map.gz | 55.8 MB | EMDB map data format | |
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Header (meta data) | emd-21113-v30.xml emd-21113.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21113_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_21113.png | 94.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21113 | HTTPS FTP |
-Validation report
Summary document | emd_21113_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_21113_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_21113_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21113 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21113 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21113.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | VPS13 protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Chaetomium thermophilum VPS13 1-1390
Entire | Name: Chaetomium thermophilum VPS13 1-1390 |
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Components |
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-Supramolecule #1: Chaetomium thermophilum VPS13 1-1390
Supramolecule | Name: Chaetomium thermophilum VPS13 1-1390 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Molecular weight | Theoretical: 161.84 kDa/nm |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: Expi293F |
-Macromolecule #1: Vacuolar protein sorting-associate protein 13
Macromolecule | Name: Vacuolar protein sorting-associate protein 13 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDHDGDY KDHDIDYKDD DDKLAAA LE GLVAGLLNRF LGMYVKNFDP KQLKWEVWNG KVRLDNLELQ REALDQLKLP INVIKGHLGH LVLHIPW KT LASEQVKINI EDVFLLASPK EEAEYDEDEE ARRRHRLKME KLDSAELLKE RSQEGLSEEE QKRTQTFA Q ...String: MDYKDHDGDY KDHDIDYKDD DDKLAAA LE GLVAGLLNRF LGMYVKNFDP KQLKWEVWNG KVRLDNLELQ REALDQLKLP INVIKGHLGH LVLHIPW KT LASEQVKINI EDVFLLASPK EEAEYDEDEE ARRRHRLKME KLDSAELLKE RSQEGLSEEE QKRTQTFA Q ALVTKIVDNL QITIRNIHIR YEDAISAPGH PFALGITLEE FSAVSTDSDW TPAFITSIQS AHKLATLES LAIYWDTDAK LIGPGREPHE HSDQIPHDEM LKFFREMIAK GEADLSSEHQ FILKPVSGQA KIEIDKTGSH TVPRYKANL LFDEIGVVLD DQQYRDALMM VDLFHYFIRH QEYKKFQPKG VTPKEDPRAW FRFAGNAVLS K IHERNRRW SWDYFRERRD DRRRYIELFK KTKQNIQLTP EEREDLDKLE WKLSYEDLRF WRSLARNQLK KE NAEALKN KPPPQPQQQQ GWLSWVWGSK PVQPQQEEQQ GDENTRITEA QRKELYEVIQ WDEKAALAAE IDV PRDSVR LLIETSLSTG SFTLRQNPHG DARDLISLHF DLFRAKGLTR PDSFLIDISL GGFRVNDNTT PDSL YKEIV RVKDAPNTEG QKRYSIADLE LTVDEEAFFE LQVEQHPLDG QGDVAVTMKL KPLEIIWNPN VVVGI ADFF RPPERHMESI NALLETANAT VEGLRAQTRA GLQFALEEHK TVNAKLDLQA PLIILPESIT TPNSTC LIV DAGHISVNSE LVDKETMKQV QSTQDRPCTE EDLRRLEELM YDRFLVKLTS TQVLIGPSVE ITKQQLV QR DEKRQLHIVD QINLDFVVAM SILPKAPNLT KLKISGHLPV LQVNASDSKY KHLMRIIEVA IPKLYDVE P VLAPSGSHPT IRPRLASDAS TRSRRASFRK ASTQFLQFVS QQQEIVLDES DSDDDSEKFE DAKDTSVDE QLRIQQRIFD FKFTVDQLRG SLYRSDPEGK HPDQLLVELV AENFGVEYHL RPYDMSAMVS LGSVTMDDFV ENPPAEFKS IVSSGDIEDR KQARDLVRVK FVRVKKESPE FMSVYDGIET NVDVAISTIN LVVTRKTLLT L LDFILVTF SNPQPAAPVA TRMAVTDQES ETNIIVQPPP IESGPIRVKV DLKSIRMILN NDGIRLATLS FN HADVGVY ILGRYMRVSA KLGDLSLVDD VNLGVSEDSS LRQLVTIQGN ELADFRYEYF DPDKPEKNPG YDS SIYLRA GSVKVNFIEE PFRKIVDFLV KFGKMQAIYN AARMAAANQA QQLQQSQSRI KFDIVVKTPI VVFP RVVMS PKPKRDVITA YLGEIYAQNA FVPLDDSEKA DMAMKLTTGI RNIRLTSHFH YSEGRDEVLE LIDHV DLGF TIIYAEHKEG IKRPDLEIEG SMSDFNLRIT PYQLSALLAI SQSVPTVFAA DVEQHT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |