[English] 日本語
Yorodumi
- EMDB-4702: Thermus thermophilus V/A-type ATPase/synthase, rotational state 1L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4702
TitleThermus thermophilus V/A-type ATPase/synthase, rotational state 1L
Map dataA combined map from focused refinements of several domains of the intact complex as described in the paper
Sample
  • Complex: Thermus thermophilus V/A-type ATPase/ATP synthase
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
KeywordsATP hydrolysis/synthesis / proton translocation / rotary catalysis / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATPase binding ...proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATPase binding / ATP binding / metal ion binding
Similarity search - Function
ATPase, V0 complex, c subunit / : / V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d ...ATPase, V0 complex, c subunit / : / V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / 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-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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type ATP synthase subunit D / V-type ATP synthase subunit E / V-type ATP synthase subunit C / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain / V-type ATP synthase, subunit (VAPC-THERM) / V-type ATP synthase subunit I / V-type ATP synthase, subunit K
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhou L / Sazanov L
CitationJournal: Science / Year: 2019
Title: Structure and conformational plasticity of the intact V/A-type ATPase.
Authors: Long Zhou / Leonid A Sazanov /
Abstract: V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the ...V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the rotary-catalysis mechanism. They belong to the V-type ATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthases in overall architecture. We solved cryo-electron microscopy structures of the intact V/A-ATPase, reconstituted into lipid nanodiscs, in three rotational states and two substates. These structures indicate substantial flexibility between V and V in a working enzyme, which results from mechanical competition between central shaft rotation and resistance from the peripheral stalks. We also describe details of adenosine diphosphate inhibition release, V-V torque transmission, and proton translocation, which are relevant for the entire V-type ATPase family.
History
DepositionMar 13, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseAug 28, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6r0z
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4702.png

Downloads & links

-
Map

FileDownload / File: emd_4702.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA combined map from focused refinements of several domains of the intact complex as described in the paper
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 131 pix.
= 142.135 Å		1.09 Å/pix.
x 132 pix.
= 143.22 Å		1.09 Å/pix.
x 236 pix.
= 256.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.14550732 - 0.3142792
Average (Standard dev.)0.0044397004 (±0.018239465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions132236131
Spacing131132236
CellA: 142.13501 Å / B: 143.22 Å / C: 256.06 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z131132236
origin x/y/z0.0000.0000.000
length x/y/z142.135143.220256.060
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ131132236
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS236132131
D min/max/mean-0.1460.3140.004

-
Supplemental data

-
Sample components

+
Entire : Thermus thermophilus V/A-type ATPase/ATP synthase

EntireName: Thermus thermophilus V/A-type ATPase/ATP synthase
Components
  • Complex: Thermus thermophilus V/A-type ATPase/ATP synthase
    • Protein or peptide: V-type ATP synthase alpha chain
    • Protein or peptide: V-type ATP synthase beta chain
    • Protein or peptide: V-type ATP synthase subunit D
    • Protein or peptide: V-type ATP synthase subunit F
    • Protein or peptide: V-type ATP synthase, subunit (VAPC-THERM)
    • Protein or peptide: V-type ATP synthase subunit E
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: Thermus thermophilus V/A-type ATPase/ATP synthase

SupramoleculeName: Thermus thermophilus V/A-type ATPase/ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 94.2 MDa

+
Macromolecule #1: V-type ATP synthase alpha chain

MacromoleculeName: V-type ATP synthase alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 63.69998 KDa
SequenceString: MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV ...String:
MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV EEPVVVLEDG TELKMYHTWP VRRARPVQRK LDPNTPFLTG MRILDVLFPV AMGGTAAIPG PFGSGKTVTQ QS LAKWSNA DVVVYVGCGE RGNEMTDVLV EFPELTDPKT GGPLMHRTVL IANTSNMPVA AREASIYVGV TIAEYFRDQG FSV ALMADS TSRWAEALRE ISSRLEEMPA EEGYPPYLAA RLAAFYERAG KVITLGGEEG AVTIVGAVSP PGGDMSEPVT QSTL RIVGA FWRLDASLAF RRHFPAINWN GSYSLFTSAL DPWYRENVAE DYPELRDAIS ELLQREAGLQ EIVQLVGPDA LQDAE RLVI EVGRIIREDF LQQNAYHEVD AYCSMKKAYG IMKMILAFYK EAEAAIKRGV SIDEILQLPV LERIGRARYV SEEEFP AYF EEAMKEIQGA FKALA

UniProtKB: V-type ATP synthase alpha chain

+
Macromolecule #2: V-type ATP synthase beta chain

MacromoleculeName: V-type ATP synthase beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 53.2195 KDa
SequenceString: MDLLKKEYTG ITYISGPLLF VENAKDLAYG AIVDIKDGTG RVRGGQVIEV SEEYAVIQVF EETTGLDLAT TSVSLVEDVA RLGVSKEML GRRFNGIGKP IDGLPPITPE KRLPITGLPL NPVARRKPEQ FIQTGISTID VMNTLVRGQK LPIFSGSGLP A NEIAAQIA ...String:
MDLLKKEYTG ITYISGPLLF VENAKDLAYG AIVDIKDGTG RVRGGQVIEV SEEYAVIQVF EETTGLDLAT TSVSLVEDVA RLGVSKEML GRRFNGIGKP IDGLPPITPE KRLPITGLPL NPVARRKPEQ FIQTGISTID VMNTLVRGQK LPIFSGSGLP A NEIAAQIA RQATVRPDLS GEGEKEEPFA VVFAAMGITQ RELSYFIQEF ERTGALSRSV LFLNKADDPT IERILTPRMA LT VAEYLAF EHDYHVLVIL TDMTNYCEAL REIGAAREEI PGRRGYPGYM YTDLATIYER AGVVEGKKGS VTQIPILSMP DDD RTHPIP DLTGYITEGQ IQLSRELHRK GIYPPIDPLP SLSRLMNNGV GKGKTREDHK QVSDQLYSAY ANGVDIRKLV AIIG EDALT ENDRRYLQFA DAFERFFINQ GQQNRSIEES LQIAWALLSM LPQGELKRIS KDHIGKYYGQ KLEEIWGAPQ ALD

UniProtKB: V-type ATP synthase beta chain

+
Macromolecule #3: V-type ATP synthase subunit D

MacromoleculeName: V-type ATP synthase subunit D / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 24.715566 KDa
SequenceString: MSQVSPTRMN LLQRRGQLRL AQKGVDLLKK KRDALVAEFF GLVREAMEAR KALDQAAKEA YAALLLAQAF DGPEVVAGAA LGVPPLEGV EAEVENVWGS KVPRLKATFP DGALLSPVGT PAYTLEASRA FRRYAEALIR VANTETRLKK IGEEIKKTTR R VNALEQVV ...String:
MSQVSPTRMN LLQRRGQLRL AQKGVDLLKK KRDALVAEFF GLVREAMEAR KALDQAAKEA YAALLLAQAF DGPEVVAGAA LGVPPLEGV EAEVENVWGS KVPRLKATFP DGALLSPVGT PAYTLEASRA FRRYAEALIR VANTETRLKK IGEEIKKTTR R VNALEQVV IPGIRAQIRF IQQVLEQRER EDTFRLKRIK GKIEAREAEE EGGRPNPQVE IGAGL

UniProtKB: V-type ATP synthase subunit D

+
Macromolecule #4: V-type ATP synthase subunit F

MacromoleculeName: V-type ATP synthase subunit F / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 11.294904 KDa
SequenceString:
MAVIADPETA QGFRLAGLEG YGASSAEEAQ SLLETLVERG GYALVAVDEA LLPDPERAVE RLMRGRDLPV LLPIAGLKEA FQGHDVEGY MRELVRKTIG FDIKL

UniProtKB: V-type ATP synthase subunit F

+
Macromolecule #5: V-type ATP synthase, subunit (VAPC-THERM)

MacromoleculeName: V-type ATP synthase, subunit (VAPC-THERM) / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 13.166218 KDa
SequenceString:
MTGGLVLNAI SRAGGAMGGL GLIKSLAEKE KQLLERLEAA KKEAEERVKR AEAEAKALLE EAEAKAKALE AQYRERERAE TEALLARYR ERAEAEAKAV REKAMARLDE AVALVLKEVL P

UniProtKB: V-type ATP synthase, subunit (VAPC-THERM)

+
Macromolecule #6: V-type ATP synthase subunit E

MacromoleculeName: V-type ATP synthase subunit E / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 20.645582 KDa
SequenceString:
MSKLEAILSQ EVEAEIQALL QEAEAKAEAV KREAEEKAKA LLQARERALE AQYRAALRRA ESAGELLVAT ARTQARGEVL EEVRRRVRE ALEALPQKPE WPEVVRKLAL EALEALPGAK ALVANPEDLP HLEALARERG VELQAEPALR LGVRAVGAEG K TQVENSLL ARLDRAWDAL SSKVAQALWG

UniProtKB: V-type ATP synthase subunit E

+
Macromolecule #7: V-type ATP synthase subunit C

MacromoleculeName: V-type ATP synthase subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 35.96857 KDa
SequenceString: MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL ...String:
MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL AKRFFEDVAK AAKGLDQPAL RDYLALEVDA ENLRTAFKLQ GSGLAPDAFF LKGGRFVDRV RFARLMEGDY AV LDELSGT PFSGLSGVRD LKALERGLRC VLLKEAKKGV QDPLGVGLVL AYVKEREWEA VRLRLLARRA YFGLPRAQVE EEV VCP

UniProtKB: V-type ATP synthase subunit C

+
Macromolecule #8: V-type ATP synthase subunit I

MacromoleculeName: V-type ATP synthase subunit I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 72.204289 KDa
SequenceString: MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA ...String:
MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA HEAYAGGVAA LVVVHRKEVD QAKAALSRAG VAELRLPGAL GELPLSEAAR RLKERAEAAP RELSEVRQHL AK LARESAS TLQSLWTRAQ DEVARLKALE ELASGRFGFA LLGYVPVKAK PKVEEALARH KESVVYAFEP VDEHHEADRI PVV LDNPPW AKPFELLVSF LNTPKYGTFD PTPVVPVFFP FWFGMIVGDI GYALLFYLVG RWLSGYVKRN EPLVIDLFAL KLKP QVIGK LVHILNWMVF WTVVWGVIYG EFFGTFLEHL GVFGTPEHPG LIPILIHRID TAKTANLLIL LSVAFGVVLV FFGLA LRAY LGLKHRHMAH FWEGVGYLGG LVGVLALAAS YLGNLQAGWL QGLMYLGFGV FLLAVLMSRI WLMIPEIFTQ AGHILS HIR IYAVGAAGGI LAGLLTDVGF ALAERLGLLG VLLGLLVAGV LHLLILLLTT LGHMLQPIRL LWVEFFTKFG FYEENGR PY RPFKSVREAQ

UniProtKB: V-type ATP synthase subunit I

+
Macromolecule #9: V-type ATP synthase, subunit K

MacromoleculeName: V-type ATP synthase, subunit K / type: protein_or_peptide / ID: 9 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 9.841714 KDa
SequenceString:
MKKLLVTVLL AVFGALAFAA EEAAASGGLD RGLIAVGMGL AVGLAALGTG VAQARIGAAG VGAIAEDRSN FGTALIFLLL PETLVIFGL LIAFILNGRL

UniProtKB: V-type ATP synthase, subunit K

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMNH2C(CH2OH)3Tris
100.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride
0.1 %C32H58N2O7SCHAPS
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2700 / Average exposure time: 63.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.78 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 129032 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 181245
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5gar

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta) / Number images used: 23027
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 beta)
Final 3D classificationNumber classes: 6 / Avg.num./class: 25000 / Software - Name: RELION (ver. 3.0 beta)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5y5y

chain_id: A, residue_range: 1-578, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: B, residue_range: 1-578, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: C, residue_range: 1-578, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: D, residue_range: 5-474, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: E, residue_range: 3-471, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: F, residue_range: 3-472, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: G, residue_range: 3-209, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: H, residue_range: 1-104, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: I, residue_range: 60-120, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: J, residue_range: 2-188, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: K, residue_range: 60-120, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: L, residue_range: 2-188, source_name: PDB, initial_model_type: experimental model

5y5y

chain_id: M, residue_range: 3-322, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: N, residue_range: 1-649, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: O, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: P, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: Q, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: R, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: S, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: T, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: U, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: V, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: W, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: X, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: Y, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model

5y5x

chain_id: Z, residue_range: 8-80, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Overall B value: 112.5
Output model

PDB-6r0z:
Thermus thermophilus V/A-type ATPase/synthase, rotational state 1L

+
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