[English] 日本語
Yorodumi
- EMDB-0648: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0648
TitleSaccharomyces cerevisiae V-ATPase Stv1-V1VO State 3
Map data
Sample
  • Complex: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3
    • Protein or peptide: x 16 types
KeywordsProton pump / MEMBRANE PROTEIN
Function / homology
Function and homology information


vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly ...vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / P-type proton-exporting transporter activity / vacuolar transport / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuole organization / protein targeting to vacuole / pexophagy / fungal-type vacuole / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / phosphatidylinositol-4-phosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / ATP metabolic process / H+-transporting two-sector ATPase / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / cell periphery / transmembrane transport / intracellular calcium ion homeostasis / endocytosis / cytoplasmic stress granule / late endosome / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / endosome membrane / membrane raft / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / cytoplasm
Similarity search - Function
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 / ATPase, V1 complex, subunit A / Ribonuclease kappa / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C ...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 / ATPase, V1 complex, subunit A / Ribonuclease kappa / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / ATP synthase (E/31 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / 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 / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit f / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit C / V-type proton ATPase subunit d / V-type proton ATPase subunit D / V-type proton ATPase subunit c' ...V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit f / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit C / V-type proton ATPase subunit d / V-type proton ATPase subunit D / V-type proton ATPase subunit c' / V-type proton ATPase subunit a, Golgi isoform / V-type proton ATPase subunit F / V-type proton ATPase subunit H / V-type proton ATPase subunit G / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae (strain RM11-1a) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsVasanthakumar T / Bueler SA / Wu D / Beilsten-Edmands V / Robinson CV / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP81294 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural comparison of the vacuolar and Golgi V-ATPases from .
Authors: Thamiya Vasanthakumar / Stephanie A Bueler / Di Wu / Victoria Beilsten-Edmands / Carol V Robinson / John L Rubinstein /
Abstract: Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal ...Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V complexes containing Stv1p could be readily purified without attached V regions. We used this effect to determine structures of the membrane-embedded V region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring.
History
DepositionMar 8, 2019-
Header (metadata) releaseApr 3, 2019-
Map releaseApr 3, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o7x
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0648.png

Downloads & links

-
Map

FileDownload / File: emd_0648.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 256 pix.
= 371.2 Å		1.45 Å/pix.
x 256 pix.
= 371.2 Å		1.45 Å/pix.
x 256 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.09971295 - 0.40242386
Average (Standard dev.)0.003406137 (±0.038293824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1000.4020.003

-
Supplemental data

-
Sample components

+
Entire : Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3

EntireName: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3
Components
  • Complex: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3
    • Protein or peptide: V-type proton ATPase subunit C
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: Vacuolar ATP synthase catalytic subunit A
    • Protein or peptide: V-type proton ATPase subunit B
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase subunit E
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: V-type proton ATPase subunit a, Golgi isoform
    • Protein or peptide: V0 assembly protein 1
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: V-type proton ATPase subunit c'
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: Putative protein YPR170W-B

+
Supramolecule #1: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3

SupramoleculeName: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 44.241352 KDa
SequenceString: MATALYTAND FILISLPQNA QPVTAPGSKT DSWFNETLIG GRAFVSDFKI PEFKIGSLDT LIVESEELSK VDNQIGASIG KIIEILQGL NETSTNAYRT LPINNMPVPE YLENFQWQTR KFKLDKSIKD LITLISNESS QLDADVRATY ANYNSAKTNL A AAERKKTG ...String:
MATALYTAND FILISLPQNA QPVTAPGSKT DSWFNETLIG GRAFVSDFKI PEFKIGSLDT LIVESEELSK VDNQIGASIG KIIEILQGL NETSTNAYRT LPINNMPVPE YLENFQWQTR KFKLDKSIKD LITLISNESS QLDADVRATY ANYNSAKTNL A AAERKKTG DLSVRSLHDI VKPEDFVLNS EHLTTVLVAV PKSLKSDFEK SYETLSKNVV PASASVIAED AEYVLFNVHL FK KNVQEFT TAAREKKFIP REFNYSEELI DQLKKEHDSA ASLEQSLRVQ LVRLAKTAYV DVFINWFHIK ALRVYVESVL RYG LPPHFN IKIIAVPPKN LSKCKSELID AFGFLGGNAF MKDKKGKINK QDTSLHQYAS LVDTEYEPFV MYIINL

UniProtKB: V-type proton ATPase subunit C

+
Macromolecule #2: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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

+
Macromolecule #3: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.47917 KDa
SequenceString:
MAEKRTLIAV IADEDTTTGL LLAGIGQITP ETQEKNFFVY QEGKTTKEEI TDKFNHFTEE RDDIAILLIN QHIAENIRAR VDSFTNAFP AILEIPSKDH PYDPEKDSVL KRVRKLFGE

UniProtKB: V-type proton ATPase subunit F

+
Macromolecule #4: Vacuolar ATP synthase catalytic subunit A

MacromoleculeName: Vacuolar ATP synthase catalytic subunit A / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain RM11-1a) (yeast) / Strain: RM11-1a
Molecular weightTheoretical: 70.515203 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 AIIYVGCGER GNEMAEVLME FPELYTEMSG TKEPIMKRTT LVA NTSNMP VAAREASIYT GITLAEYFRD QGKNVSMIAD SSSRWAEALR EISGRLGEMP ADQGFPAYLG AKLASFYERA GKAV ALGSP DRTGSVSIVA AVSPAGGDFS DPVTTATLGI TQVFWGLDKK LAQRKHFPSI NTSVSYSKYT NVLNKFYDSN YPEFP VLRD RMKEILSNAE ELEQVVQLVG KSALSDSDKI TLDVATLIKE DFLQQNGYST YDAFCPIWKT FDMMRAFISY HDEAQK AVA NGANWSKLAD STGDVKHAVS SSKFFEPSRG EKEVHGEFEK LLSTMQERFA ESTDDYKDHD GDYKDHDIDY KDDDDK

UniProtKB: V-type proton ATPase catalytic subunit A

+
Macromolecule #5: V-type proton ATPase subunit B

MacromoleculeName: V-type proton ATPase subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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

+
Macromolecule #6: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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

+
Macromolecule #7: V-type proton ATPase subunit E

MacromoleculeName: V-type proton ATPase subunit E / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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

+
Macromolecule #8: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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

+
Macromolecule #9: V-type proton ATPase subunit a, Golgi isoform

MacromoleculeName: V-type proton ATPase subunit a, Golgi isoform / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 101.762438 KDa
SequenceString: MNQEEAIFRS ADMTYVQLYI PLEVIREVTF LLGKMSVFMV MDLNKDLTAF QRGYVNQLRR FDEVERMVGF LNEVVEKHAA ETWKYILHI DDEGNDIAQP DMADLINTME PLSLENVNDM VKEITDCESR ARQLDESLDS LRSKLNDLLE QRQVIFECSK F IEVNPGIA ...String:
MNQEEAIFRS ADMTYVQLYI PLEVIREVTF LLGKMSVFMV MDLNKDLTAF QRGYVNQLRR FDEVERMVGF LNEVVEKHAA ETWKYILHI DDEGNDIAQP DMADLINTME PLSLENVNDM VKEITDCESR ARQLDESLDS LRSKLNDLLE QRQVIFECSK F IEVNPGIA GRATNPEIEQ EERDVDEFRM TPDDISETLS DAFSFDDETP QDRGALGNDL TRNQSVEDLS FLEQGYQHRY MI TGSIRRT KVDILNRILW RLLRGNLIFQ NFPIEEPLLE GKEKVEKDCF IIFTHGETLL KKVKRVIDSL NGKIVSLNTR SSE LVDTLN RQIDDLQRIL DTTEQTLHTE LLVIHDQLPV WSAMTKREKY VYTTLNKFQQ ESQGLIAEGW VPSTELIHLQ DSLK DYIET LGSEYSTVFN VILTNKLPPT YHRTNKFTQA FQSIVDAYGI ATYKEINAGL ATVVTFPFMF AIMFGDMGHG FILFL MALF LVLNERKFGA MHRDEIFDMA FTGRYVLLLM GAFSVYTGLL YNDIFSKSMT IFKSGWQWPS TFRKGESIEA KKTGVY PFG LDFAWHGTDN GLLFSNSYKM KLSILMGYAH MTYSFMFSYI NYRAKNSKVD IIGNFIPGLV FMQSIFGYLS WAIVYKW SK DWIKDDKPAP GLLNMLINMF LAPGTIDDQL YSGQAKLQVV LLLAALVCVP WLLLYKPLTL RRLNKNGGGG RPHGYQSV G NIEHEEQIAQ QRHSAEGFQG MIISDVASVA DSINESVGGG EQGPFNFGDV MIHQVIHTIE FCLNCISHTA SYLRLWALS LAHAQLSSVL WDMTISNAFS SKNSGSPLAV MKVVFLFAMW FVLTVCILVF MEGTSAMLHA LRLHWVEAMS KFFEGEGYAY EPFSFRAII E

UniProtKB: V-type proton ATPase subunit a, Golgi isoform

+
Macromolecule #10: V0 assembly protein 1

MacromoleculeName: V0 assembly protein 1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 29.694885 KDa
SequenceString: MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK ...String:
MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK SGDNLTVVIN SLGWAFEDED GDDEYATEET LSHHDNNKGK EGDDDILSSI WTEGLLMCLI VSALLLFILI VA LSWISNL DITYGALEKS TNPIKKNN

UniProtKB: V0 assembly protein 1

+
Macromolecule #11: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.610641 KDa
SequenceString: MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA ...String:
MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA TAAISDAADS ALFVKILVIE IFGSILGLLG LIVGLLMAGK ASEFQ

UniProtKB: V-type proton ATPase subunit c''

+
Macromolecule #12: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.822484 KDa
SequenceString: MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT ...String:
MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT AEELDDMNIE IIRNKLYKAY LEDFYNFVTE EIPEPAKECM QTLLGFEADR RSINIALNSL QSSDIDPDLK SD LLPNIGK LYPLATFHLA QAQDFEGVRA ALANVYEYRG FLETGNLEDH FYQLEMELCR DAFTQQFAIS TVWAWMKSKE QEV RNITWI AECIAQNQRE RINNYISVY

UniProtKB: V-type proton ATPase subunit d

+
Macromolecule #13: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 13 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.357501 KDa
SequenceString:
MTELCPVYAP FFGAIGCASA IIFTSLGAAY GTAKSGVGIC ATCVLRPDLL FKNIVPVIMA GIIAIYGLVV SVLVCYSLGQ KQALYTGFI QLGAGLSVGL SGLAAGFAIG IVGDAGVRGS SQQPRLFVGM ILILIFAEVL GLYGLIVALL LNSRATQDVV C

UniProtKB: V-type proton ATPase subunit c

+
Macromolecule #14: V-type proton ATPase subunit c'

MacromoleculeName: V-type proton ATPase subunit c' / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.046361 KDa
SequenceString:
MSTQLASNIY APLYAPFFGF AGCAAAMVLS CLGAAIGTAK SGIGIAGIGT FKPELIMKSL IPVVMSGILA IYGLVVAVLI AGNLSPTED YTLFNGFMHL SCGLCVGFAC LSSGYAIGMV GDVGVRKYMH QPRLFVGIVL ILIFSEVLGL YGMIVALILN T RGSE

UniProtKB: V-type proton ATPase subunit c'

+
Macromolecule #15: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.387065 KDa
SequenceString:
MSSFYTVVGV FIVVSAMSVL FWIMAPKNNQ AVWRSTVILT LAMMFLMWAI TFLCQLHPLV APRRSDLRPE FAE

UniProtKB: V-type proton ATPase subunit e

+
Macromolecule #16: Putative protein YPR170W-B

MacromoleculeName: Putative protein YPR170W-B / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 9.369934 KDa
SequenceString:
MRPVVSTGKA WCCTVLSAFG VVILSVIAHL FNTNHESFVG SINDPEDGPA VAHTVYLAAL VYLVFFVFCG FQVYLARRKP SIELR

UniProtKB: V-type proton ATPase subunit f

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7283
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more