[English] 日本語
Yorodumi
- EMDB-8409: Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8409
TitleAtomic model for the membrane-embedded motor of a eukaryotic V-ATPase
Map dataAtomic model for the membrane-embedded motor of a eukaryotic V-ATPase
Sample
  • Complex: Vo region of the V-ATPase from Saccharomyces cerevisiae
    • Protein or peptide: V-type proton ATPase subunit a
    • 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 c
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: V-type proton ATPase subunit f
    • Protein or peptide: V-type proton ATPase subunit d
KeywordsRotary ATPase / Vacuolar-type ATPase / Electron Cryomicroscopy / Vo region / Membrane protein / MOTOR PROTEIN
Function / homology
Function and homology information


cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification ...cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / protein targeting to vacuole / vacuole organization / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / cellular hyperosmotic response / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / membrane
Similarity search - Function
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 ...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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit d / V-type proton ATPase subunit a, vacuolar isoform / V-type proton ATPase subunit c' / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMazhab-Jafari MT / Rohou A / Schmidt C / Bueler SA / Benlekbir S / Robinson CV / Rubinstein JL
Funding support Canada, United Kingdom, European Union, 4 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP81294 Canada
Wellcome TrustWT008150 United Kingdom
Wellcome TrustWT099141 United Kingdom
European Research Council (ERC)ERC268851European Union
CitationJournal: Nature / Year: 2016
Title: Atomic model for the membrane-embedded V motor of a eukaryotic V-ATPase.
Authors: Mohammad T Mazhab-Jafari / Alexis Rohou / Carla Schmidt / Stephanie A Bueler / Samir Benlekbir / Carol V Robinson / John L Rubinstein /
Abstract: Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney ...Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V region drives proton translocation through the membrane-embedded V region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V and V regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the V complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits acc'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.
History
DepositionOct 12, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseOct 26, 2016-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5tj5
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8409.png

Downloads & links

-
Map

FileDownload / File: emd_8409.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAtomic model for the membrane-embedded motor of a eukaryotic V-ATPase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.55 Å/pix.
x 200 pix.
= 310.8 Å		1.55 Å/pix.
x 200 pix.
= 310.8 Å		1.55 Å/pix.
x 200 pix.
= 310.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.554 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0475 / Movie #1: 0.07
Minimum - Maximum-0.15724738 - 0.27012172
Average (Standard dev.)-0.0014383988 (±0.010948882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 310.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5541.5541.554
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z310.800310.800310.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1570.270-0.001

-
Supplemental data

-
Sample components

-
Entire : Vo region of the V-ATPase from Saccharomyces cerevisiae

EntireName: Vo region of the V-ATPase from Saccharomyces cerevisiae
Components
  • Complex: Vo region of the V-ATPase from Saccharomyces cerevisiae
    • Protein or peptide: V-type proton ATPase subunit a
    • 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 c
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: V-type proton ATPase subunit f
    • Protein or peptide: V-type proton ATPase subunit d

-
Supramolecule #1: Vo region of the V-ATPase from Saccharomyces cerevisiae

SupramoleculeName: Vo region of the V-ATPase from Saccharomyces cerevisiae
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 300 KDa

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

MacromoleculeName: V-type proton ATPase subunit a / 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: 70.067984 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)AQYRE INAGLPTIVT FPFMFAIMFG DMGHG FLMT LAALSLVLNE KKINKMKRGE IFDMAFTGRY IILLMGVFSM YTGFLYNDIF SKTMTIFKSG WKWPDHWKKG ESITAT SVG TYPIGLDWAW HGTENALLFS NSYKMKLSIL MGFIHMTYSY FFSLANHLYF NSMIDIIGNF IPGLLFMQGI FGYLSVC IV YKWAVDWVKD GKPAPGLLNM LINMFLSPGT IDDELYPHQA KVQVFLLLMA LVCIPWLLLV KPLHFKFTHK KKSHEPLP S TEADASSEDL EAQQLISAMD ADDAEEEEVG SGSHGEDFGD IMIHQVIHTI EFCLNCVSHT ASYLRLWALS LAHAQLSSV LWTMTIQIAF GFRGFVGVFM TVALFAMWFA LTCAVLVLME GTSAMLHSLR LHWVESMSKF FVGEGLPYEP FAFEYKDMEV

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

-
Macromolecule #2: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / 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: 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 #3: V-type proton ATPase subunit c'

MacromoleculeName: V-type proton ATPase subunit c' / 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: 15.195271 KDa
SequenceString:
FFGFAGCAAA MVLSCLGAAI GTAKSGIGIA GIGTFKPELI MKSLIPVVMS GILAIYGLVV AVLIAGNLSP TEDYTLFNGF MHLSCGLCV GFACLSSGYA IGMVGDVGVR KYMHQPRLFV GIVLILIFSE VLGLYGMIVA LILNTRGS

UniProtKB: V-type proton ATPase subunit c'

-
Macromolecule #4: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.218087 KDa
SequenceString:
APFFGAIGCA SAIIFTSLGA AYGTAKSGVG ICATCVLRPD LLFKNIVPVI MAGIIAIYGL VVSVLVCYSL GQKQALYTGF IQLGAGLSV GLSGLAAGFA IGIVGDAGVR GSSQQPRLFV GMILILIFAE VLGLYGLIVA LLLNSRATQD V

UniProtKB: V-type proton ATPase subunit c

-
Macromolecule #5: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 6.476928 KDa
SequenceString:
YTVVGVFIVV SAMSVLFWIM APKNNQAVWR STVILTLAMM FLMWAITFLC QLHPLVA

UniProtKB: V-type proton ATPase subunit e

-
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 4.613678 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

-
Macromolecule #7: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 32.854238 KDa
SequenceString: VYFNIDNGFI EGVVRGYRNG LLSNNQYINL TQCDTLEDLK LQLSSTDYGN FLSSVSSESL TTSLIQEYAS SKLYHEFNYI RDQSSGSTR KFMDYITYGY MIDNVALMIT GTIHDRDKGE ILQRCHPLGW FDTLPTLSVA TDLESLYETV LVD(UNK) (UNK)(UNK)(UNK) ...String:
VYFNIDNGFI EGVVRGYRNG LLSNNQYINL TQCDTLEDLK LQLSSTDYGN FLSSVSSESL TTSLIQEYAS SKLYHEFNYI RDQSSGSTR KFMDYITYGY MIDNVALMIT GTIHDRDKGE ILQRCHPLGW FDTLPTLSVA TDLESLYETV LVD(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)NIEII RNKLYKAYLE DFYNFVTEEI P(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)LEDHF YQLEMELCRD AFTQQFAIST VWAWMKSKEQ EVRNITWIAE CIAQNQRERI NNY

UniProtKB: V-type proton ATPase subunit d, V-type proton ATPase subunit d, V-type proton ATPase subunit d

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
Details: 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin
GridModel: Maxtaform / Material: COPPER/RHODIUM / Mesh: 400 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.3 K / Instrument: FEI VITROBOT MARK III / Details: Modified for ethane/propane.
DetailsThe Vo region was solubilized in amphipol A8-35 (Anatrace)

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Details70 micro meter objective aperture, illuminated area of 1.58 micro meter diameter
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 4365 / Average exposure time: 21.0 sec. / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.4 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 64350 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsImages were recorded in "super-resolution" mode and then resampled by Fourier cropping.
Particle selectionNumber selected: 657975
Startup modelType of model: OTHER / Details: An in-house map of the Vo region.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11)
Details: Data beyond 6 A resolution were omitted from refinement.
Number images used: 462842
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Merit function: Weighted correlation coefficient
Projection matching processing - Angular sampling: 3.4 degrees
Software - Name: FREALIGN (ver. 9.11)
Details: Frealign exhaustive search (mode 3; i.e. projection matching followed by local refinement of top solutions)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Merit function: Weighted correlation coefficient
Software - Name: FREALIGN (ver. 9.11) / Details: Refinement with Frealign mode 1.

-
Atomic model buiding 1

Detailsphenix.real_space_refine REFINEMENT TARGET: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) MODEL TO MAP FIT. CC(ACROSS WHOLE MAP VOLUME): 0.6772 CC(ONLY ACROSS ATOMS IN THE MODEL): 0.6842
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-5tj5:
Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase

+
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