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- EMDB-45789: Yeast RAVE complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45789
TitleYeast RAVE complex
Map dataThe original primary map was highly anisotropic, so it was low-pass filtered to a resolution of 12 A. The unfiltered map is also included as an additional map.
Sample
  • Complex: yeast RAVE complex
    • Protein or peptide: Rav1p
    • Protein or peptide: Rav2p
    • Protein or peptide: Skp1p
KeywordsRAVE / assembly / CHAPERONE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsWang H / Rubinstein JL
Funding support United States, Canada, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R35GM145256 United States
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure of yeast RAVE bound to a partial V complex.
Authors: Hanlin Wang / Maureen Tarsio / Patricia M Kane / John L Rubinstein /
Abstract: Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes ...Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes consist of a soluble catalytic V subcomplex and a membrane-embedded proton-translocating V subcomplex. The V and V subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V and V requiring the protein complex known as RAVE (regulator of the ATPase of vacuoles and endosomes). In the yeast , RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V. In the structure, RAVE is an L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V. Only Rav1p interacts with V, binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V is in a rotational state suitable for binding the free V complex, but in the structure, it is partially disrupted, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V complex with RAVE appears poised for reassembly with V.
History
DepositionJul 17, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45789.png

Downloads & links

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Map

FileDownload / File: emd_45789.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe original primary map was highly anisotropic, so it was low-pass filtered to a resolution of 12 A. The unfiltered map is also included as an additional map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.36068696 - 0.6551732
Average (Standard dev.)0.00037837512 (±0.01693494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Original unfiltered map

Fileemd_45789_additional_1.map
AnnotationOriginal unfiltered map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45789_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45789_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast RAVE complex

EntireName: yeast RAVE complex
Components
  • Complex: yeast RAVE complex
    • Protein or peptide: Rav1p
    • Protein or peptide: Rav2p
    • Protein or peptide: Skp1p

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Supramolecule #1: yeast RAVE complex

SupramoleculeName: yeast RAVE complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Rav1p

MacromoleculeName: Rav1p / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSLNFLPGRP NATPQTACQ A TWQNHTIF AY CSGNNLI ILT NKFTRL QTIY TQSDC TAVDI NSQN GFIALS FHN RVLIYKP IH QIMQNPKW T QCCQLFHDD TPVNCLRWSS DNELAIGSD F LSFWKIKD NF GVYQPIL QWN QKQPKP VYNV IISQD ...String:
MSLNFLPGRP NATPQTACQ A TWQNHTIF AY CSGNNLI ILT NKFTRL QTIY TQSDC TAVDI NSQN GFIALS FHN RVLIYKP IH QIMQNPKW T QCCQLFHDD TPVNCLRWSS DNELAIGSD F LSFWKIKD NF GVYQPIL QWN QKQPKP VYNV IISQD SQLIV SIGK YDCNAK LWK RVSIVGE QA IFNLTMLP H PKPITAMRW KKEPDQVSKN NTASHALYT L CEDKVLRI WS CFEMEKN HTV QIWGEV PLSP TQKFC VIIDN WIIR QTLSVK DSE IFDISDS DI VILGSMTG E MEVLALNNL SQDPPKPMTK KTISHKKVK K ATMLNDTR YL YLPEIQP YDN VKGKLS FLVH DLQGV IRHLL IDIL QLINNK TED LSAALEH KF TGHNKSVQ K LVRSSDGEA LLTTSRFSEN GVWYPQKLN H GVSLRLQN TI QTESPIK FAV VHELGK QVIC LLENG ALQAW ECPT NRKEDS EQK QSYLRVE TR LKEEKKIH P IVMLNTPEP KHSHERHFTA LIFSDGSIK A FEVSLTRG IF EVKSDSL DID GDDIYK ISII DPVHQ TFVSN RPLI SLITKK GLT RTYKAIV NY NDRHVQWI K ACEINTGIM NCTCIRGSST GKLCIVNST G KVMSLWDL NR GVLEYEE TFH NPIEDI DWTS TEYGQ SIVSI GFTG YALLYT QLR YDYTNNT PS YLPIEKID I TAHTAHNIG DSVWMKNGTF VVASGNQFY I KDKSLDLT DP FTYQSIG SRK ILSNDI LHLS SVLNG PLPVY HPQF LIQAIY ANK LQLVKEL LL RLFLALRK L DFESQDVSN LDSNLGMDPL KYFIAKDRD Y PVESFPDP YP CFNKTVS LAL TEQLTK TTLP YLTRH QQITL ITVI EAVDEV TKN ENIVDYN GV RFLLGVKL F LSHKNIQKS ILMRDVSWAL HSDNKEILL S SIDRHITS WN RAREYRI AYW IKEQDL VKKF EDIAK YEFSK DDKR DPSRCA IFY LALKKKQ IL LSLWKMAI G HPEQQKMVR FISNDFTVPR WRTAALKNA F VLLSKHRY MD AAVFFLL TDS LKDCVN VLCK QVHDM DLAIG VCRV YEGDNG PVL GELLTAQ ML PETIKEND R WKASFIYWK LRKQEVAIKA LLTAPIDLE N NSSIVDKE VC VNRSFLV EDP ALLYLY NHLR NRNLK YFIGS LNVE AKIECT LIL RVTDILC RM GCNYLAVS L VKNWKFIER NSIPVQKLLK SPTKDRAYS A IGAMASEP IS TARMRPS LFD KFGSPS ASDI ESPNP KLPNS LLDD FLQPPP NST SSNSLAQ SS SSAPRSIL D EFVSPSYSQ HKENLTPKAP NDSVGETDN S ENRKDKLS KD ILDDLSS QKP QKPKKS AITK NLLDD FV

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Macromolecule #2: Rav2p

MacromoleculeName: Rav2p / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSVDLFPNDR FGAEDKYDN F KDAVKECS WL IEEIVKP QLP NIIDNF SKCL EMLES DQIFK MPVS NGIPNE SNK QNDSPTV KG VITRQGQY I VDFHIVVRF PQFQRGKQVM FRMNTGLNF L LIQFSKIM TH LKNILEI LNQ LQVATD VSEF VSKFG ...String:
MSVDLFPNDR FGAEDKYDN F KDAVKECS WL IEEIVKP QLP NIIDNF SKCL EMLES DQIFK MPVS NGIPNE SNK QNDSPTV KG VITRQGQY I VDFHIVVRF PQFQRGKQVM FRMNTGLNF L LIQFSKIM TH LKNILEI LNQ LQVATD VSEF VSKFG VAMEL LNHS LILLQN PPR DLVFPED NN FAMKEMFQ D CYSVCESTA HILGLELTLC RNELCIELR N LIKVTKKP WC EIDSKTG RSF CDQIRN QVTN ERNKT LSKIL SENG VQVQDS TLL NHIISSF QS EAITLPEA Q ELLRRGVTF DNRVVMECEK LIVSTSDPT L ISISAKLN SL KASMANH QAN LVASKQ LSTY K

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Macromolecule #3: Skp1p

MacromoleculeName: Skp1p / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVTSNVVLVS GEGERFTVD K KIAERSLL LK NYLNDMH DSN LQNNSD SESD SDSET NHKSK DNNN GDDDDE DDD EIVMPVP NV RSSVLQKV I EWAEHHRDS NFPDEDDDDS RKSAPVDSW D REFLKVDQ EM LYEIILA ANY LNIKPL LDAG CKVVA ...String:
MVTSNVVLVS GEGERFTVD K KIAERSLL LK NYLNDMH DSN LQNNSD SESD SDSET NHKSK DNNN GDDDDE DDD EIVMPVP NV RSSVLQKV I EWAEHHRDS NFPDEDDDDS RKSAPVDSW D REFLKVDQ EM LYEIILA ANY LNIKPL LDAG CKVVA EMIRG RSPE EIRRTF NIV NDFTPEE EA AIRRENEW A EDR

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92040
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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