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- EMDB-27442: Cryo-EM structure of a HOPS core complex containing Vps33, Vps16,... -

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Basic information

Entry
Database: EMDB / ID: EMD-27442
TitleCryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18
Map dataCryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18
Sample
  • Complex: HOPS core complex
    • Complex: His-Vps33:Vps16
      • Protein or peptide: Vacuolar protein sorting-associated protein 33Vacuole
      • Protein or peptide: Vacuolar protein sorting-associated protein 16Vacuole
    • Complex: Vps18
      • Protein or peptide: Vacuolar protein sorting-associated protein 18Vacuole
KeywordsHOPS / membrane tethering / SNAREs / membrane fusion / endolysosomal trafficking / PROTEIN TRANSPORT
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsPort SA / Farrell PD / Jeffrey PD / DiMaio F / Hughson FM
Funding support Germany, United States, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)PO2195/1-1 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123089 United States
CitationJournal: 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
DepositionJun 29, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27442.png

Downloads & links

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Map

FileDownload / File: emd_27442.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18
Voxel sizeX=Y=Z: 1.426 Å
Density
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-0.7477457 - 2.0704396
Average (Standard dev.)0.00054051046 (±0.065924495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 513.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_27442_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_27442_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HOPS core complex

EntireName: HOPS core complex
Components
  • Complex: HOPS core complex
    • Complex: His-Vps33:Vps16
      • Protein or peptide: Vacuolar protein sorting-associated protein 33Vacuole
      • Protein or peptide: Vacuolar protein sorting-associated protein 16Vacuole
    • Complex: Vps18
      • Protein or peptide: Vacuolar protein sorting-associated protein 18Vacuole

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Supramolecule #1: HOPS core complex

SupramoleculeName: HOPS core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 171 KDa

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Supramolecule #2: His-Vps33:Vps16

SupramoleculeName: His-Vps33:Vps16 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Supramolecule #3: Vps18

SupramoleculeName: Vps18 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Macromolecule #1: Vacuolar protein sorting-associated protein 33

MacromoleculeName: Vacuolar protein sorting-associated protein 33 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 77.119617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Vacuolar protein sorting-associated protein 16

MacromoleculeName: Vacuolar protein sorting-associated protein 16 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 94.204828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: Vacuolar protein sorting-associated protein 18

MacromoleculeName: Vacuolar protein sorting-associated protein 18 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 108.52757 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.08 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
150.0 mMNaClSodium chloridesodium chloride
1.0 mMDTTDTT
GridModel: 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
VitrificationCryogen 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.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.03 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4092244 / Details: blob picker 60-280A (circular)
Startup modelType of model: OTHER / Details: AbInitio model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 130000 / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2.15.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
cryoSPARC (ver. 2.15.0)
RELION (ver. 3.1.0)pixel refinement

Number images used: 154917
FSC plot (resolution estimation)

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