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- EMDB-45788: Yeast RAVE bound to V-ATPase V1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45788
TitleYeast RAVE bound to V-ATPase V1 complex
Map data
Sample
  • Complex: Yeast RAVE bound to V-ATPase V1 complex
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
KeywordsV-ATPase / RAVE / assembly / HYDROLASE
Function / homology
Function and homology information


RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / : / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / vacuole-mitochondrion membrane contact site / septin ring assembly / Insulin receptor recycling ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / : / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / vacuole-mitochondrion membrane contact site / septin ring assembly / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / vacuolar proton-transporting V-type ATPase, V1 domain / early endosome to late endosome transport / endosomal lumen acidification / regulation of exit from mitosis / proton-transporting V-type ATPase complex / kinetochore assembly / pexophagy / intron homing / intein-mediated protein splicing / exit from mitosis / vacuolar proton-transporting V-type ATPase complex / positive regulation of D-glucose transmembrane transport / vacuolar acidification / protein neddylation / fungal-type vacuole membrane / mitotic intra-S DNA damage checkpoint signaling / mitochondrial fusion / silent mating-type cassette heterochromatin formation / regulation of metabolic process / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / DNA replication origin binding / proton-transporting ATPase activity, rotational mechanism / regulation of protein-containing complex assembly / subtelomeric heterochromatin formation / H+-transporting two-sector ATPase / ATP metabolic process / negative regulation of cytoplasmic translation / Neutrophil degranulation / endomembrane system / proton transmembrane transport / regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / kinetochore / transmembrane transport / G2/M transition of mitotic cell cycle / intracellular calcium ion homeostasis / cytoplasmic stress granule / protein transport / mitotic cell cycle / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / early endosome membrane / endonuclease activity / Hydrolases; Acting on ester bonds / chromosome, telomeric region / protein ubiquitination / membrane raft / Golgi membrane / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / membrane / cytoplasm
Similarity search - Function
RAVE complex protein Rav1 C-terminal / : / RAVE protein 1 C terminal / RAVE subunit 2/Rogdi / Rogdi leucine zipper containing protein / Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / ATPase, V1 complex, subunit H ...RAVE complex protein Rav1 C-terminal / : / RAVE protein 1 C terminal / RAVE subunit 2/Rogdi / Rogdi leucine zipper containing protein / Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / Intein / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / SKP1/BTB/POZ domain superfamily / Armadillo-like helical / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit B / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E / V-type proton ATPase subunit D / V-type proton ATPase subunit F / V-type proton ATPase subunit H / Regulator of V-ATPase in vacuolar membrane protein 1 / V-type proton ATPase subunit G / Suppressor of kinetochore protein 1 / Regulator of V-ATPase in vacuolar membrane protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang H / Rubinstein JL
Funding support United States, Canada, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)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-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45788.png

Downloads & links

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Map

FileDownload / File: emd_45788.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 390 pix.
= 401.7 Å		1.03 Å/pix.
x 390 pix.
= 401.7 Å		1.03 Å/pix.
x 390 pix.
= 401.7 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: 0.1
Minimum - Maximum-2.7796712 - 5.182949
Average (Standard dev.)-0.000053142503 (±0.09581577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions390390390
Spacing390390390
CellA=B=C: 401.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast RAVE bound to V-ATPase V1 complex

EntireName: Yeast RAVE bound to V-ATPase V1 complex
Components
  • Complex: Yeast RAVE bound to V-ATPase V1 complex
    • Protein or peptide: V-type proton ATPase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit B
    • Protein or peptide: V-type proton ATPase subunit E
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: Regulator of V-ATPase in vacuolar membrane protein 1
    • Protein or peptide: Regulator of V-ATPase in vacuolar membrane protein 2
    • Protein or peptide: Suppressor of kinetochore protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Yeast RAVE bound to V-ATPase V1 complex

SupramoleculeName: Yeast RAVE bound to V-ATPase V1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: V-type proton ATPase catalytic subunit A

MacromoleculeName: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 118.782547 KDa
SequenceString: MAGAIENARK EIKRISLEDH AESEYGAIYS VSGPVVIAEN MIGCAMYELV KVGHDNLVGE VIRIDGDKAT IQVYEETAGL TVGDPVLRT GKPLSVELGP GLMETIYDGI QRPLKAIKEE SQSIYIPRGI DTPALDRTIK WQFTPGKFQV GDHISGGDIY G SVFENSLI ...String:
MAGAIENARK EIKRISLEDH AESEYGAIYS VSGPVVIAEN MIGCAMYELV KVGHDNLVGE VIRIDGDKAT IQVYEETAGL TVGDPVLRT GKPLSVELGP GLMETIYDGI QRPLKAIKEE SQSIYIPRGI DTPALDRTIK WQFTPGKFQV GDHISGGDIY G SVFENSLI SSHKILLPPR SRGTITWIAP AGEYTLDEKI LEVEFDGKKS DFTLYHTWPV RVPRPVTEKL SADYPLLTGQ RV LDALFPC VQGGTTCIPG AFGCGKTVIS QSLSKYSNSD AIIYVGCFAK GTNVLMADGS IECIENIEVG NKVMGKDGRP REV IKLPRG RETMYSVVQK SQHRAHKSDS SREVPELLKF TCNATHELVV RTPRSVRRLS RTIKGVEYFE VITFEMGQKK APDG RIVEL VKEVSKSYPI SEGPERANEL VESYRKASNK AYFEWTIEAR DLSLLGSHVR KATYQTYAPI LYENDHFFDY MQKSK FHLT IEGPKVLAYL LGLWIGDGLS DRATFSVDSR DTSLMERVTE YAEKLNLCAE YKDRKEPQVA KTVNLYSKVV RGNGIR NNL NTENPLWDAI VGLGFLKDGV KNIPSFLSTD NIGTRETFLA GLIDSDGYVT DEHGIKATIK TIHTSVRDGL VSLARSL GL VVSVNAEPAK VDMNGTKHKI SYAIYMSGGD VLLNVLSKCA GSKKFRPAPA AAFARECRGF YFELQELKED DYYGITLS D DSDHQFLLAN QVVVHNCGER GNEMAEVLME FPELYTEMSG TKEPIMKRTT LVANTSNMPV AAREASIYTG ITLAEYFRD QGKNVSMIAD SSSRWAEALR EISGRLGEMP ADQGFPAYLG AKLASFYERA GKAVALGSPD RTGSVSIVAA VSPAGGDFSD PVTTATLGI TQVFWGLDKK LAQRKHFPSI NTSVSYSKYT NVLNKFYDSN YPEFPVLRDR MKEILSNAEE LEQVVQLVGK S ALSDSDKI TLDVATLIKE DFLQQNGYST YDAFCPIWKT FDMMRAFISY HDEAQKAVAN GANWSKLADS TGDVKHAVSS SK FFEPSRG EKEVHGEFEK LLSTMQERFA ESTD

UniProtKB: V-type proton ATPase catalytic subunit A

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Macromolecule #2: V-type proton ATPase subunit B

MacromoleculeName: V-type proton ATPase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 57.815023 KDa
SequenceString: MVLSDKELFA INKKAVEQGF NVKPRLNYNT VSGVNGPLVI LEKVKFPRYN EIVNLTLPDG TVRQGQVLEI RGDRAIVQVF EGTSGIDVK KTTVEFTGES LRIPVSEDML GRIFDGSGRP IDNGPKVFAE DYLDINGSPI NPYARIYPEE MISTGVSAID T MNSIARGQ ...String:
MVLSDKELFA INKKAVEQGF NVKPRLNYNT VSGVNGPLVI LEKVKFPRYN EIVNLTLPDG TVRQGQVLEI RGDRAIVQVF EGTSGIDVK KTTVEFTGES LRIPVSEDML GRIFDGSGRP IDNGPKVFAE DYLDINGSPI NPYARIYPEE MISTGVSAID T MNSIARGQ KIPIFSASGL PHNEIAAQIC RQAGLVRPTK DVHDGHEENF SIVFAAMGVN LETARFFKQD FEENGSLERT SL FLNLAND PTIERIITPR LALTTAEYLA YQTERHVLTI LTDMSSYADA LREVSAAREE VPGRRGYPGY MYTDLSTIYE RAG RVEGRN GSITQIPILT MPNDDITHPI PDLTGYITEG QIFVDRQLHN KGIYPPINVL PSLSRLMKSA IGEGMTRKDH GDVS NQLYA KYAIGKDAAA MKAVVGEEAL SIEDKLSLEF LEKFEKTFIT QGAYEDRTVF ESLDQAWSLL RIYPKEMLNR ISPKI LDEF YDRARDDADE DEEDPDTRSS GKKKDASQEE SLI

UniProtKB: V-type proton ATPase subunit B

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Macromolecule #3: V-type proton ATPase subunit E

MacromoleculeName: V-type proton ATPase subunit E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 26.508393 KDa
SequenceString: MSSAITALTP NQVNDELNKM QAFIRKEAEE KAKEIQLKAD QEYEIEKTNI VRNETNNIDG NFKSKLKKAM LSQQITKSTI ANKMRLKVL SAREQSLDGI FEETKEKLSG IANNRDEYKP ILQSLIVEAL LKLLEPKAIV KALERDVDLI ESMKDDIMRE Y GEKAQRAP ...String:
MSSAITALTP NQVNDELNKM QAFIRKEAEE KAKEIQLKAD QEYEIEKTNI VRNETNNIDG NFKSKLKKAM LSQQITKSTI ANKMRLKVL SAREQSLDGI FEETKEKLSG IANNRDEYKP ILQSLIVEAL LKLLEPKAIV KALERDVDLI ESMKDDIMRE Y GEKAQRAP LEEIVISNDY LNKDLVSGGV VVSNASDKIE INNTLEERLK LLSEEALPAI RLELYGPSKT RKFFD

UniProtKB: V-type proton ATPase subunit E

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Macromolecule #4: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.738706 KDa
SequenceString:
MSQKNGIATL LQAEKEAHEI VSKARKYRQD KLKQAKTDAA KEIDSYKIQK DKELKEFEQK NAGGVGELEK KAEAGVQGEL AEIKKIAEK KKDDVVKILI ETVIKPSAEV HINAL

UniProtKB: V-type proton ATPase subunit G

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Macromolecule #5: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 29.235023 KDa
SequenceString: MSGNREQVFP TRMTLGLMKT KLKGANQGYS LLKRKSEALT KRFRDITKRI DDAKQKMGRV MQTAAFSLAE VSYATGENIG YQVQESVST ARFKVRARQE NVSGVYLSQF ESYIDPEIND FRLTGLGRGG QQVQRAKEIY SRAVETLVEL ASLQTAFIIL D EVIKVTNR ...String:
MSGNREQVFP TRMTLGLMKT KLKGANQGYS LLKRKSEALT KRFRDITKRI DDAKQKMGRV MQTAAFSLAE VSYATGENIG YQVQESVST ARFKVRARQE NVSGVYLSQF ESYIDPEIND FRLTGLGRGG QQVQRAKEIY SRAVETLVEL ASLQTAFIIL D EVIKVTNR RVNAIEHVII PRTENTIAYI NSELDELDRE EFYRLKKVQE KKQNETAKLD AEMKLKRDRA EQDASEVAAD EE PQGETLV ADQEDDVIF

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #6: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.347975 KDa
SequenceString:
AEKRTLIAVI ADEDTTTGLL LAGIGQITPE TQEKNFFVYQ EGKTTKEEIT DKFNHFTEER DDIAILLINQ HIAENIRARV DSFTNAFPA ILEIPSKDHP YDPEKDSVLK RVRKLFGE

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #7: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 54.482609 KDa
SequenceString: MGATKILMDS THFNEIRSII RSRSVAWDAL ARSEELSEID ASTAKALESI LVKKNIGDGL SSSNNAHSGF KVNGKTLIPL IHLLSTSDN EDCKKSVQNL IAELLSSDKY GDDTVKFFQE DPKQLEQLFD VSLKGDFQTV LISGFNVVSL LVQNGLHNVK L VEKLLKNN ...String:
MGATKILMDS THFNEIRSII RSRSVAWDAL ARSEELSEID ASTAKALESI LVKKNIGDGL SSSNNAHSGF KVNGKTLIPL IHLLSTSDN EDCKKSVQNL IAELLSSDKY GDDTVKFFQE DPKQLEQLFD VSLKGDFQTV LISGFNVVSL LVQNGLHNVK L VEKLLKNN NLINILQNIE QMDTCYVCIR LLQELAVIPE YRDVIWLHEK KFMPTLFKIL QRATDSQLAT RIVATNSNHL GI QLQYHSL LLIWLLTFNP VFANELVQKY LSDFLDLLKL VKITIKEKVS RLCISIILQC CSTRVKQHKK VIKQLLLLGN ALP TVQSLS ERKYSDEELR QDISNLKEIL ENEYQELTSF DEYVAELDSK LLCWSPPHVD NGFWSDNIDE FKKDNYKIFR QLIE LLQAK VRNGDVNAKQ EKIIIQVALN DITHVVELLP ESIDVLDKTG GKADIMELLN HSDSRVKYEA LKATQAIIGY TFK

UniProtKB: V-type proton ATPase subunit H

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Macromolecule #8: Regulator of V-ATPase in vacuolar membrane protein 1

MacromoleculeName: Regulator of V-ATPase in vacuolar membrane protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 155.127328 KDa
SequenceString: MSLNFLPGRP NATPQTACQA TWQNHTIFAY CSGNNLIILT NKFTRLQTIY TQSDCTAVDI NSQNGFIALS FHNRVLIYKP IHQIMQNPK WTQCCQLFHD DTPVNCLRWS SDNELAIGSD FLSFWKIKDN FGVYQPILQW NQKQPKPVYN VIISQDSQLI V SIGKYDCN ...String:
MSLNFLPGRP NATPQTACQA TWQNHTIFAY CSGNNLIILT NKFTRLQTIY TQSDCTAVDI NSQNGFIALS FHNRVLIYKP IHQIMQNPK WTQCCQLFHD DTPVNCLRWS SDNELAIGSD FLSFWKIKDN FGVYQPILQW NQKQPKPVYN VIISQDSQLI V SIGKYDCN AKLWKRVSIV GEQAIFNLTM LPHPKPITAM RWKKEPDQVS KNNTASHALY TLCEDKVLRI WSCFEMEKNH TV QIWGEVP LSPTQKFCVI IDNWIIRQTL SVKDSEIFDI SDSDIVILGS MTGEMEVLAL NNLSQDPPKP MTKKTISHKK VKK ATMLND TRYLYLPEIQ PYDNVKGKLS FLVHDLQGVI RHLLIDILQL INNKTEDLSA ALEHKFTGHN KSVQKLVRSS DGEA LLTTS RFSENGVWYP QKLNHGVSLR LQNTIQTESP IKFAVVHELG KQVICLLENG ALQAWECPTN RKEDSEQKQS YLRVE TRLK EEKKIHPIVM LNTPEPKHSH ERHFTALIFS DGSIKAFEVS LTRGIFEVKS DSLDIDGDDI YKISIIDPVH QTFVSN RPL ISLITKKGLT RTYKAIVNYN DRHVQWIKAC EINTGIMNCT CIRGSSTGKL CIVNSTGKVM SLWDLNRGVL EYEETFH NP IEDIDWTSTE YGQSIVSIGF TGYALLYTQL RYDYTNNTPS YLPIEKIDIT AHTAHNIGDS VWMKNGTFVV ASGNQFYI K DKSLDLTDPF TYQSIGSRKI LSNDILHLSS VLNGPLPVYH PQFLIQAIYA NKLQLVKELL LRLFLALRKL DFESQDVSN LDSNLGMDPL KYFIAKDRDY PVESFPDPYP CFNKTVSLAL TEQLTKTTLP YLTRHQQITL ITVIEAVDEV TKNENIVDYN GVRFLLGVK LFLSHKNIQK SILMRDVSWA LHSDNKEILL SSIDRHITSW NRAREYRIAY WIKEQDLVKK FEDIAKYEFS K DDKRDPSR CAIFYLALKK KQILLSLWKM AIGHPEQQKM VRFISNDFTV PRWRTAALKN AFVLLSKHRY MDAAVFFLLT DS LKDCVNV LCKQVHDMDL AIGVCRVYEG DNGPVLGELL TAQMLPETIK ENDRWKASFI YWKLRKQEVA IKALLTAPID LEN NSSIVD KEVCVNRSFL VEDPALLYLY NHLRNRNLKY FIGSLNVEAK IECTLILRVT DILCRMGCNY LAVSLVKNWK FIER NSIPV QKLLKSPTKD RAYSAIGAMA SEPISTARMR PSLFDKFGSP SASDIESPNP KLPNSLLDDF LQPPPNSTSS NSLAQ SSSS APRSILDEFV SPSYSQHKEN LTPKAPNDSV GETDNSENRK DKLSKDILDD LSSQKPQKPK KSAITKNLLD DFV

UniProtKB: Regulator of V-ATPase in vacuolar membrane protein 1

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Macromolecule #9: Regulator of V-ATPase in vacuolar membrane protein 2

MacromoleculeName: Regulator of V-ATPase in vacuolar membrane protein 2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 40.061035 KDa
SequenceString: MSVDLFPNDR FGAEDKYDNF KDAVKECSWL IEEIVKPQLP NIIDNFSKCL EMLESDQIFK MPVSNGIPNE SNKQNDSPTV KGVITRQGQ YIVDFHIVVR FPQFQRGKQV MFRMNTGLNF LLIQFSKIMT HLKNILEILN QLQVATDVSE FVSKFGVAME L LNHSLILL ...String:
MSVDLFPNDR FGAEDKYDNF KDAVKECSWL IEEIVKPQLP NIIDNFSKCL EMLESDQIFK MPVSNGIPNE SNKQNDSPTV KGVITRQGQ YIVDFHIVVR FPQFQRGKQV MFRMNTGLNF LLIQFSKIMT HLKNILEILN QLQVATDVSE FVSKFGVAME L LNHSLILL QNPPRDLVFP EDNNFAMKEM FQDCYSVCES TAHILGLELT LCRNELCIEL RNLIKVTKKP WCEIDSKTGR SF CDQIRNQ VTNERNKTLS KILSENGVQV QDSTLLNHII SSFQSEAITL PEAQELLRRG VTFDNRVVME CEKLIVSTSD PTL ISISAK LNSLKASMAN HQANLVASKQ LSTYK

UniProtKB: Regulator of V-ATPase in vacuolar membrane protein 2

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Macromolecule #10: Suppressor of kinetochore protein 1

MacromoleculeName: Suppressor of kinetochore protein 1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.35727 KDa
SequenceString: MVTSNVVLVS GEGERFTVDK KIAERSLLLK NYLNDMHDSN LQNNSDSESD SDSETNHKSK DNNNGDDDDE DDDEIVMPVP NVRSSVLQK VIEWAEHHRD SNFPDEDDDD SRKSAPVDSW DREFLKVDQE MLYEIILAAN YLNIKPLLDA GCKVVAEMIR G RSPEEIRR ...String:
MVTSNVVLVS GEGERFTVDK KIAERSLLLK NYLNDMHDSN LQNNSDSESD SDSETNHKSK DNNNGDDDDE DDDEIVMPVP NVRSSVLQK VIEWAEHHRD SNFPDEDDDD SRKSAPVDSW DREFLKVDQE MLYEIILAAN YLNIKPLLDA GCKVVAEMIR G RSPEEIRR TFNIVNDFTP EEEAAIRREN EWAEDR

UniProtKB: Suppressor of kinetochore protein 1

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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
GridModel: Homemade / Material: COPPER/RHODIUM
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: 42.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71341
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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