[English] 日本語
Yorodumi
- EMDB-21353: Mammalian V-ATPase from rat brain collar and peripheral stalks ro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21353
TitleMammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement)
Map dataMammalian rat brain V-ATPase with SidK bound, focused refinement of the collar and membrane proximal regions conformational state 3
Sample
  • Complex: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a isoform 1
Keywordsmembrane protein complex / rotary atpase / PROTON TRANSPORT
Function / homology
Function and homology information


Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / intracellular organelle / clathrin-coated vesicle membrane ...Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / intracellular organelle / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / transmembrane transporter complex / regulation of macroautophagy / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / terminal bouton / synaptic vesicle membrane / melanosome / synaptic vesicle / apical part of cell / ATPase binding / endosome / apical plasma membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V0 complex, subunit 116kDa, eukaryotic / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit
Similarity search - Domain/homology
V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit C 1 / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsAbbas YM / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Science / Year: 2020
Title: Structure of V-ATPase from the mammalian brain.
Authors: Yazan M Abbas / Di Wu / Stephanie A Bueler / Carol V Robinson / John L Rubinstein /
Abstract: In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes ...In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a effector protein. Cryo-electron microscopy allowed the construction of an atomic model, defining the enzyme's ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme's catalytic and membrane regions.
History
DepositionFeb 5, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseMar 18, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vqk
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vqk
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21353.png

Downloads & links

-
Map

FileDownload / File: emd_21353.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMammalian rat brain V-ATPase with SidK bound, focused refinement of the collar and membrane proximal regions conformational state 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 340 pix.
= 360.4 Å		1.06 Å/pix.
x 340 pix.
= 360.4 Å		1.06 Å/pix.
x 340 pix.
= 360.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.0123566 - 2.4945457
Average (Standard dev.)-0.00046290064 (±0.06429877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 360.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z360.400360.400360.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-1.0122.495-0.000

-
Supplemental data

-
Sample components

-
Entire : Peripheral stalk and collar region of mammalian V-ATPase composed...

EntireName: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
Components
  • Complex: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a isoform 1

-
Supramolecule #1: Peripheral stalk and collar region of mammalian V-ATPase composed...

SupramoleculeName: Peripheral stalk and collar region of mammalian V-ATPase composed of subunits E1, G2, N-terminal domain of a1, and C1.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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

MacromoleculeName: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.958453 KDa
SequenceString: MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLASGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE ...String:
MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLASGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE IVKKDDFVLD SEYLVTLLVV VPKLNHNDWI KQYETLAEMV VPRSSNVLSE DQDSYLCNVT LFKKAVDDFR HK ARENKFI VRDFQYNEEE MRADKEEMNR LSTDKKKQFG PLVRWLKVNF SEAFIAWIHI KALRVFVESV LRYGLPVNFQ AML LQPNKK SVKKLREVLH ELYKHLDSSA AAIIDAPMDI PGLNLSQQEY YPYVYYKIDC NLLEFK

UniProtKB: V-type proton ATPase subunit C 1

-
Macromolecule #2: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 26.167453 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K KDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K KDVDVQID LEAYLPEDIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

-
Macromolecule #3: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 13.690476 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVADARKRKA RRLKQAKEEA QMEVEQYRRE REQEFQSKQQ AAMGSQGNLS AEVEQATRRQ VQGMQSSQQ RNRERVLTQL LGMVCDVRPQ VHPNYRITV

UniProtKB: V-type proton ATPase subunit G

-
Macromolecule #4: V-type proton ATPase 116 kDa subunit a isoform 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 96.429438 KDa
SequenceString: MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL ...String:
MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL GFVAGVINRE RIPTFERMLW RVCRGNVFLR QAEIENPLED PVTGDYVHKS VFIIFFQGDQ LKNRVKKICE GF RASLYPC PETPQERKEM ASGVNTRIDD LQMVLNQTED HRQRVLQAAA KNIRVWFIKV RKMKAIYHTL NLCNIDVTQK CLI AEVWCP VTDLDSIQFA LRRGTEHSGS TVPSILNRMQ TNQTPPTYNK TNKFTHGFQN IVDAYGIGTY REINPAPYTV ITFP FLFAV MFGDFGHGIL MTLFAVWMVL RESRILSQKN ENEMFSMVFS GRYIILLMGL FSIYTGLIYN DCFSKSLNIF GSSWS VRPM FTIGNWTEET LLGSSVLQLN PAIPGVFGGP YPFGIDPIWN IATNKLTFLN SFKMKMSVIL GIIHMLFGVS LSLFNH IYF KKPLNIYFGF IPEIIFMSSL FGYLVILIFY KWTAYDAHSS RNAPSLLIHF INMFLFSYPE SGNAMLYSGQ KGIQCFL IV VAMLCVPWML LFKPLILRHQ YLRKKHLGTL NFGGIRVGNG PTEEDAEIIQ HDQLSTHSED AEEPTEDEVF DFGDTMVH Q AIHTIEYCLG CISNTASYLR LWALSLAHAQ LSEVLWTMVI HIGLHVRSLA GGLGLFFIFA AFATLTVAIL LIMEGLSAF LHALRLHWVE FQNKFYTGTG FKFLPFSFEH IREGKFDE

UniProtKB: V-type proton ATPase 116 kDa subunit a 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79654
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

+
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