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- EMDB-49559: Yeast V1-ATPase bound to Rtc5p -

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Basic information

Entry
Database: EMDB / ID: EMD-49559
TitleYeast V1-ATPase bound to Rtc5p
Map dataYeast V1 bound to Rtc5p - composite map
Sample
  • Complex: Yeast V1-ATPase bound to Rtc5p
    • Protein or peptide: H(+)-transporting two-sector ATPase
    • Protein or peptide: V-type proton ATPase subunit E
    • Protein or peptide: Yeast V-ATPase subunit G
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: Restriction of telomere capping protein 5
    • Protein or peptide: V-type proton ATPase subunit B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsVacuolar ATPase / V1-ATPase / Rtc5p / protein structure / PROTON TRANSPORT
Function / homology
Function and homology information


vacuole-mitochondrion membrane contact site / 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 / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification ...vacuole-mitochondrion membrane contact site / 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 / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / pexophagy / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / proton-transporting ATPase activity, rotational mechanism / ATP metabolic process / H+-transporting two-sector ATPase / Neutrophil degranulation / proton transmembrane transport / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / response to oxidative stress / membrane raft / Golgi membrane / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit ...TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / 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 / : / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase catalytic subunit A / Restriction of telomere capping protein 5 / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit D / V-type proton ATPase subunit F
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKhan MM / Wilkens S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141908 United States
CitationJournal: To Be Published
Title: TLDc Protein Rtc5p Assembles Yeast V-ATPase
Authors: Khan MM / Wilkens S
History
DepositionMar 4, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49559.png

Downloads & links

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Map

FileDownload / File: emd_49559.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast V1 bound to Rtc5p - composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 256 pix.
= 426.24 Å		1.67 Å/pix.
x 256 pix.
= 426.24 Å		1.67 Å/pix.
x 256 pix.
= 426.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.665 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.013425309 - 0.058669537
Average (Standard dev.)0.0004477381 (±0.0014604403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast V1-ATPase bound to Rtc5p

EntireName: Yeast V1-ATPase bound to Rtc5p
Components
  • Complex: Yeast V1-ATPase bound to Rtc5p
    • Protein or peptide: H(+)-transporting two-sector ATPase
    • Protein or peptide: V-type proton ATPase subunit E
    • Protein or peptide: Yeast V-ATPase subunit G
    • Protein or peptide: V-type proton ATPase subunit D
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: Restriction of telomere capping protein 5
    • Protein or peptide: V-type proton ATPase subunit B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Yeast V1-ATPase bound to Rtc5p

SupramoleculeName: Yeast V1-ATPase bound to Rtc5p / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: H(+)-transporting two-sector ATPase

MacromoleculeName: H(+)-transporting two-sector ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 67.796508 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 ESTD

UniProtKB: V-type proton ATPase catalytic subunit A

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Macromolecule #2: V-type proton ATPase subunit E

MacromoleculeName: V-type proton ATPase subunit E / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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 #3: Yeast V-ATPase subunit G

MacromoleculeName: Yeast V-ATPase subunit G / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.73568 KDa
SequenceString:
MDYKDDDDKS QKNGIATLLQ AEKEAHEIVS KARKYRQDKL KQAKTDAAKE IDSYKIQKDK ELKEFEQKNA GGVGELEKKA EAGVQGELA EIKKIAEKKK DDVVKILIET VIKPSAEVHI NAL

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Macromolecule #4: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 4 / 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 #5: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #6: Restriction of telomere capping protein 5

MacromoleculeName: Restriction of telomere capping protein 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 64.368312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGQSSSISSS NEEGSSHSKK FTNSKDILAY FNNKAQQQVT IPELVSFKGN LQIEDLNTPI SHKALCNSLY FPQNHAMIVG IVTNMLRVL SNFPLMKSSY EPITGYGLLK CILLLNRARC AKFLKTKSYD QLKLLFISLS LQKTDKEELS EESENDGNKE L TIKQIITG ...String:
MGQSSSISSS NEEGSSHSKK FTNSKDILAY FNNKAQQQVT IPELVSFKGN LQIEDLNTPI SHKALCNSLY FPQNHAMIVG IVTNMLRVL SNFPLMKSSY EPITGYGLLK CILLLNRARC AKFLKTKSYD QLKLLFISLS LQKTDKEELS EESENDGNKE L TIKQIITG FDDVDTEMLC IPADFMLQFL TWLLILTVDC PTTNSKLDNT ETHDQWGNFK VSALNLLRTM NPDVVGDIES HS ITFQQFS TAIRTVMPNL LKPLENLMEH FFYLQHDLVD HDTNLSSIQD SKVMTPALLA QLSTGLPKEL FIHKLQSLYI GRK SGFSMR SLQAKVFKWM APSILVVSGM RITNSEEYAA EKNPRYRHFL EEFPKLKESD QMMDASHLNK RKTTFAVYID DPWK VTNKD YFGDLNTRII EISPRQDIYK VNQKGTIYFN TIGGGIGIGD KQPLIKPASK RYIPGNVSLT FDSTLEFAVF RNTGY GGSL DPGLLSMERK EENSPYELHF LIQDVEVWGC GGEKELEEQI KQLEWEEAES KRRQQINLRS LGEDRALLEM AGLVGQ HQG GGSM

UniProtKB: Restriction of telomere capping protein 5

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Macromolecule #7: V-type proton ATPase subunit B

MacromoleculeName: V-type proton ATPase subunit B / type: protein_or_peptide / ID: 7 / Number of copies: 3 / 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 #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / 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: 7.2
GridModel: C-flat-1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 279 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 49.25 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm

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Image processing

Particle selectionNumber selected: 556655
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

31541

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 67351
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)

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Atomic model buiding 1

Initial model
PDB IDChain

7tmm

source_name: PDB, initial_model_type: experimental model

9moy
PDB Unreleased entry

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9nn1:
Yeast V1-ATPase bound to Rtc5p

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