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Yorodumi- EMDB-27442: Cryo-EM structure of a HOPS core complex containing Vps33, Vps16,... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27442 | ||||||||||||
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Title | Cryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18 | ||||||||||||
Map data | Cryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18 | ||||||||||||
Sample |
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Keywords | HOPS / membrane tethering / SNAREs / membrane fusion / endolysosomal trafficking / PROTEIN TRANSPORT | ||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||||||||
Authors | Port SA / Farrell PD / Jeffrey PD / DiMaio F / Hughson FM | ||||||||||||
Funding support | Germany, United States, 3 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the HOPS core complex and its implication for SNARE assembly Authors: Port SA / Farrell PD / Jeffrey PD / DiMaio F / Hughson FM | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27442.map.gz | 164.9 MB | EMDB map data format | |
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Header (meta data) | emd-27442-v30.xml emd-27442.xml | 23.5 KB 23.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27442_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_27442.png | 114.6 KB | ||
Filedesc metadata | emd-27442.cif.gz | 7.7 KB | ||
Others | emd_27442_half_map_1.map.gz emd_27442_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27442 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27442 | HTTPS FTP |
-Validation report
Summary document | emd_27442_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_27442_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_27442_validation.xml.gz | 20 KB | Display | |
Data in CIF | emd_27442_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27442 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27442 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27442.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.426 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B
File | emd_27442_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_27442_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HOPS core complex
Entire | Name: HOPS core complex |
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Components |
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-Supramolecule #1: HOPS core complex
Supramolecule | Name: HOPS core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Molecular weight | Theoretical: 171 KDa |
-Supramolecule #2: His-Vps33:Vps16
Supramolecule | Name: His-Vps33:Vps16 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
-Supramolecule #3: Vps18
Supramolecule | Name: Vps18 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
-Macromolecule #1: Vacuolar protein sorting-associated protein 33
Macromolecule | Name: Vacuolar protein sorting-associated protein 33 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Molecular weight | Theoretical: 77.119617 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKHHHHHHHG AAGTSLYKKA GENLYFQGSM APRAGFDAEQ VRDKARKDLL HLLEGVRGKK NLVIEKDLAG PLGVIVKAST LRDYGVDNF FFLENKNTGT SQRNIVFIAR GESVRNAHAI AAQIKRIQRE SQTSHDFHIF WVPRRTLFSD KVLEEAGVLG D ANISELPL ...String: MKHHHHHHHG AAGTSLYKKA GENLYFQGSM APRAGFDAEQ VRDKARKDLL HLLEGVRGKK NLVIEKDLAG PLGVIVKAST LRDYGVDNF FFLENKNTGT SQRNIVFIAR GESVRNAHAI AAQIKRIQRE SQTSHDFHIF WVPRRTLFSD KVLEEAGVLG D ANISELPL YFFPLERDVL SLELNDSFRD LYLAKDPTPV FLLSRALMGI QKKHGLFPRI IGKGENAKRV ADLLSRMRQE LL AGEEAGE SDRAGLSPST TIESVIIIDR EVDFVTPLLT QLTYEGLIDE YFGIQNNQTD VDAVIVGAPA QSAASTSTAV PTN SSQSRK RKIQLDGSDS LYSQLRDANF AIVGSLLNTV ARRLKSDYES RHNTKTTAEL KEFVKKLPGY QAEQQSLKIH SNIA EEIIN YTRTEIFNKL LEVQQNLAAG ADPSSQFDSI EELVARDTPL PQVLRLLCLY SCISGGIKTK ELDHFRRLVL QGYGH QHLL TLHNLERLQM FLSKSSPLAS MITMSGSSGG PDQKTNYTYL RKQLRLIVDE VNEQDPNDIA YVYSGYAPLS IRLVQC VLQ KQYLLSITKG SGTVIAAGPV AGGGAQGWKG FEEIVKHARG PTFDEIQKGE DKAVKARALL SGSSGDKKTV FVVFVGG IT FTEIAALRFI AKQEEARRNI VICTTSIING NRMMNAAIET ATFEKTTVTT AAAQ |
-Macromolecule #2: Vacuolar protein sorting-associated protein 16
Macromolecule | Name: Vacuolar protein sorting-associated protein 16 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Molecular weight | Theoretical: 94.204828 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDTAHPTASW EQLGERFYRK IQLYTQVFDQ DFDLDNYIVT GAPYGGAIAL YRDDEKLVAY QPSRSSRPTI DICSLSGKLL RRISWDQGP IKGVGWSEDE KLLIVMVDGT VRCYFDLQSE FTQFSLGHGA EEHGVKSCRF YSHGLVALLG NNALVSVSSY D EPRPKLLA ...String: MDTAHPTASW EQLGERFYRK IQLYTQVFDQ DFDLDNYIVT GAPYGGAIAL YRDDEKLVAY QPSRSSRPTI DICSLSGKLL RRISWDQGP IKGVGWSEDE KLLIVMVDGT VRCYFDLQSE FTQFSLGHGA EEHGVKSCRF YSHGLVALLG NNALVSVSSY D EPRPKLLA SPPEGRVYSW NIIPPAYSLS RSVEVLLSVN QTIYVCDASE CEDRFLDIGP FSHIAVSPNG RFCALYTTTG KV HVITSDF QSRLSEHDTK SKIAPNYFEW CGNDAVVIAW DDEVHLVGPS GSLARFFYDS GRIHLIPDFD GVRILANDRC DFL QKVPDV IEEVFGLGAD SPASILLDAV EQLEMKSPKA DDNIQLIRPH LVEAVDTCVS AAGQEFSIHW QKQLLKAASF GKSV LDIYN SDDFVDMCET LRVLNAVRFY EVGLPLSYEQ YQRLSPSGLI SRLLNRHEYL LAIRIADHLR LPTDKIHVHW ASAKV RLGS EDDDTICRKI VEKLSGKPGI SFEVIARTAY EEGRTRLATE LLNHEPRAGR QVPLLLSMEE DELALDKAIE SGDTDL IYF VIHQLRRKLP LASFFRVVSS RPTASAMVEA LARNSDGDGN EDTALLKDLY YQDDRRLDGA SVFIREALQQ PETRTAS DK LDLAANLLQG NQKEHVFELG ALKEAKMLLR MQETFERDLT DSFVGLSVNQ TMFKLIKLGY HGRAKKIQSE FKVPERVA W WIRLQALVAK RDWNEIEEIS RQRKSPIGWE PFFNQVLQAG NPRLAATFIP KCTNLEPGQT ITMYEKCGMR VKAAEEAVR LKDTEAWNRL LEAAGRNTAE GREIERLGAT VFKK |
-Macromolecule #3: Vacuolar protein sorting-associated protein 18
Macromolecule | Name: Vacuolar protein sorting-associated protein 18 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Molecular weight | Theoretical: 108.52757 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MALDLSSGFA AADAIANLQL ADATLPIFEV LPVQLQFSVA ADFVAGQAAN NVLVIALSNG RILRIDLNKP EDIDDIDLPK KPSEVGVIR RMFLDPTASH LIICTSLGEN YYLHSQSRQP RPLARLRGVV IESIAWSPAL PTQSTREILI GAADGNIYEA Y IETSTEFY ...String: MALDLSSGFA AADAIANLQL ADATLPIFEV LPVQLQFSVA ADFVAGQAAN NVLVIALSNG RILRIDLNKP EDIDDIDLPK KPSEVGVIR RMFLDPTASH LIICTSLGEN YYLHSQSRQP RPLARLRGVV IESIAWSPAL PTQSTREILI GAADGNIYEA Y IETSTEFY RREDKYLKLV QKLPDGPITG LWADSLPGHK DTRRVLVATS SRLFHWVGKI GRGHDSGGGA SIYDKLFEAE QP TVHALSG ASAAAMSMLV VSPDAEQPSP RFREDEVPER AFAWLSSHGV YHGKLLLKGP LSELGAKVFA EAKLLPRAQL ANP EGASRR QLSTEYVDAV ALTQWHIVSL VAGRVVIANR LTGSIIYDQT ILNPGQKAVG LCVDQQKSTF WLFTPQEIFE IVPR DEDRD IWKIMLQLQQ FDAALQYAHT PAEKDAVAIA SGDHLVSKGQ FLEAAAVYGK SSKPFEEVAL TFIDNEQPDA LRKYL LTKL GTYKKSAVMQ RVMIATWLIE VFMAKLNSLD DTIITGAELS ETLNPNQTKE QLEAVRAEFQ DFINKHKGDL DRKTVY DVI GSHGREEELL YYANAINDYN YVLSYWVQRE RWTEALKVLK KQTDPEVFYR YSSVLMTHAA TELVEILMRQ SNLNPRN LI PAMLEYDRNY KGPLAQNQAV RYLLYVVNQL GSTDSAVHNT LVSIYASHPS KDESALLEYL ESQGEEPNYD PDFALRLC I QHRRVLSCAH IYTSMGQYGA AVDLALAHDE VELASIIADR PISNPQLRKK LWLKVAKKVI SQQSDGIKTA IDFLRRCDL LKIEDLIPFF PDFVVIDDFK EEICAALEDY SRNIDALRRE MDEASQTAAN IKVDIAALDK RYAIVEPGEK CYACGLPLLS RQFFVFPCQ HAFHSDCLAR RVLEQAPPAK ARRIKECQVQ ISKGLVNGEK REAMIAELDA LIASACDYAI RRINEPFIKD D DDKDEWAL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.08 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: PELCO Easiglow, 10 mA/ 10 s discharge/ 30 s hold | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: Blotting parameters: 30 seconds waiting time, blotting force 1, blot total 1. |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 3590 / Average exposure time: 5.6 sec. / 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: 0.03 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |