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- EMDB-13186: F1Fo-ATP synthase from Acinetobacter baumannii (state 3) -

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Basic information

Entry
Database: EMDB / ID: EMD-13186
TitleF1Fo-ATP synthase from Acinetobacter baumannii (state 3)
Map dataCryo-em map of ATP synthase from A. baumannii (state 3).
Sample
  • Complex: F1Fo ATP synthase
    • Protein or peptide: x 8 types
  • Ligand: x 3 types
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal 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 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit a / ATP synthase subunit c / ATP synthase subunit b / ATP synthase subunit delta / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 17978 (bacteria) / Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsDemmer JK / Phillips BP / Uhrig OL / Filloux A / Allsopp LP / Bublitz M / Meier T
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome TrustWT110068/Z/15/Z United Kingdom
CitationJournal: Sci Adv / Year: 2022
Title: Structure of ATP synthase from ESKAPE pathogen .
Authors: Julius K Demmer / Ben P Phillips / O Lisa Uhrig / Alain Filloux / Luke P Allsopp / Maike Bublitz / Thomas Meier /
Abstract: The global spread of multidrug-resistant infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the FF-adenosine 5'-triphosphate ...The global spread of multidrug-resistant infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the FF-adenosine 5'-triphosphate (ATP) synthase from in three distinct conformational states. The nucleotide-converting F subcomplex reveals a specific self-inhibition mechanism, which supports a unidirectional ratchet mechanism to avoid wasteful ATP consumption. In the membrane-embedded F complex, the structure shows unique structural adaptations along both the entry and exit pathways of the proton-conducting a-subunit. These features, absent in mitochondrial ATP synthases, represent attractive targets for the development of next-generation therapeutics that can act directly at the culmination of bioenergetics in this clinically relevant pathogen.
History
DepositionJul 8, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0377
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0377
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p3w
  • Surface level: 0.0377
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p3w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13186.png

Downloads & links

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Map

FileDownload / File: emd_13186.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-em map of ATP synthase from A. baumannii (state 3).
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.0377 / Movie #1: 0.0377
Minimum - Maximum-0.061589103 - 0.17448203
Average (Standard dev.)0.0004428845 (±0.007692622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 382.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z382.500382.500382.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0620.1740.000

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Supplemental data

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Sample components

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Entire : F1Fo ATP synthase

EntireName: F1Fo ATP synthase
Components
  • Complex: F1Fo ATP synthase
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: F1Fo ATP synthase

SupramoleculeName: F1Fo ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Details: State 1 of F1Fo ATP synthase from ESKAPE pathogen Acinetobacter baumannii
Source (natural)Organism: Acinetobacter baumannii ATCC 17978 (bacteria) / Location in cell: Cell membrane
Molecular weightTheoretical: 528 KDa

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 55.452906 KDa
SequenceString: MQQLNPSEIS ALIKQRIGDL DTSATAKNEG TIVMVSDGIV RIHGLADAMY GEMIEFDGGL FGMALNLEQD SVGAVVLGNY LSLQEGQKA RCTGRVLEVP VGPELLGRVV DALGNPIDGK GPIDAKLTDA VEKVAPGVIW RQSVDQPVQT GYKSVDTMIP V GRGQRELI ...String:
MQQLNPSEIS ALIKQRIGDL DTSATAKNEG TIVMVSDGIV RIHGLADAMY GEMIEFDGGL FGMALNLEQD SVGAVVLGNY LSLQEGQKA RCTGRVLEVP VGPELLGRVV DALGNPIDGK GPIDAKLTDA VEKVAPGVIW RQSVDQPVQT GYKSVDTMIP V GRGQRELI IGDRQTGKTA MAIDAIIAQK NSGIKCVYVA IGQKQSTIAN VVRKLEETGA MAYTTVVAAA AADPAAMQYL AP YSGCTMG EYFRDRGEDA LIIYDDLSKQ AVAYRQISLL LRRPPGREAY PGDVFYLHSR LLERASRVSA EYVEKFTNGA VTG KTGSLT ALPIIETQAG DVSAFVPTNV ISITDGQIFL ETSLFNAGIR PAVNAGISVS RVGGSAQTKI IKKLSGGIRT ALAQ YRELA AFAQFASDLD EATRKQLEHG QRVTELMKQK QYAPYSIADQ AVSVYASNEG YMADVEVKKI VDFDAALIAY FRSEY APLM KQIDETGDYN KDIEAAIKAG IESFKATQTY

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Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 50.32718 KDa
SequenceString: MSSGRIIQII GAVIDVEFER TSVPKIYDAL QVDGTETTLE VQQQLGDGVV RTIAMGSTEG LKRGLTVTST NAPISVPVGT ATLGRIMDV LGRPIDEAGP VATEERLPIH RQAPSYAEQA ASTDLLETGI KVIDLLCPFA KGGKVGLFGG AGVGKTVNMM E LINNIAKA ...String:
MSSGRIIQII GAVIDVEFER TSVPKIYDAL QVDGTETTLE VQQQLGDGVV RTIAMGSTEG LKRGLTVTST NAPISVPVGT ATLGRIMDV LGRPIDEAGP VATEERLPIH RQAPSYAEQA ASTDLLETGI KVIDLLCPFA KGGKVGLFGG AGVGKTVNMM E LINNIAKA HSGLSVFAGV GERTREGNDF YHEMKDSNVL DKVAMVYGQM NEPPGNRLRV ALTGLTMAEY FRDEKDENGK GR DVLLFVD NIYRYTLAGT EVSALLGRMP SAVGYQPTLA EEMGVLQERI TSTKSGSITS IQAVYVPADD LTDPSPATTF AHL DATVVL SRDIASSGIY PAIDPLDSTS RQLDPLVVGQ EHYEIARAVQ NVLQRYKELK DIIAILGMDE LAEEDKLVVY RARK IQRFF SQPFHVAEVF TGAPGKLVPL KETIRGFKGL LAGEYDHIPE QAFYMVGGID EVIAKAEKL

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Macromolecule #3: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 8.363021 KDa
SequenceString:
MELTLGLVAI ASAILIAFGA LGTAIGFGLL GGRFLEAVAR QPELAPQLQT RMFLIAGLLD AVPMIGVGIG LFFIFANPFV G

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Macromolecule #4: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 32.467396 KDa
SequenceString: MAAEEHALTS TEYIKHHLTN MTYGKMPDGT WKLAETAEEA HSMGFTAIHL DSMGWSIGLG VIFCLLFWIV ARAANAGVPT KFQSAIEMI IEFVDSSVRD TFHGKSRLIA PLALTIFVWI FLMNLMDLIP VDWIPQVAAF VGANVFGMDP HHVYFKIVPS T DPNITLGM ...String:
MAAEEHALTS TEYIKHHLTN MTYGKMPDGT WKLAETAEEA HSMGFTAIHL DSMGWSIGLG VIFCLLFWIV ARAANAGVPT KFQSAIEMI IEFVDSSVRD TFHGKSRLIA PLALTIFVWI FLMNLMDLIP VDWIPQVAAF VGANVFGMDP HHVYFKIVPS T DPNITLGM SLSVFVLILF YSIREKGVGG FVGELALNPF NPSNPVAKAL LIPVNLILEL VTFLARPISL ALRLFGNMYA GE LIFILIA LLPFWIQWAL SVPWAIFHIL VITLQAFIFM MLTIVYLSMA SEKH

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Macromolecule #5: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 17.009312 KDa
SequenceString:
MNINLTLIGQ AIAFAFFVAF CMKFVWPPLI NAISERQRKI ADGLNAAEKA KADLADAQAQ VKQELDAAKA QAAQLIEQAN RRAAQLIEE ARTQAAAEGE RIRQQAKEAV DQEINSAREE LRQQVAALAV TGAEKILNQQ VDAEAHNAML SQLAAKL

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Macromolecule #6: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 19.52501 KDa
SequenceString:
MAELLTLARP YAKAAFAYAS EQGATDNWSN ALQVLSAAVQ DEAFSAYLNR PELTPAEQVK LFAKVLGEDQ SQAVSNFLTL LADNDRLVL LPEIAAEYEQ LKSQNNNNVD VVIESAFPLT AEQEQLLKSA LEKRFNSTVT VSVEVKPELI AGVVIRAGDQ V IDDSALNK LEKMRTRLLA

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Macromolecule #7: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 14.551682 KDa
SequenceString:
MATMQCDVVS VKESIYSGAV TMLIAKGAGG ELGILPGHAP LVTLLQPGPI RVLLENGTEE IVYVSGGVLE VQPHVVTVLA DTAIRADNL DEAAILEARK NAEQLLANQK SDLDSAAALA ALAETAAQLE TIRKIKNRAQ

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Macromolecule #8: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Molecular weightTheoretical: 32.135037 KDa
SequenceString: MANLKEIRAK VASIKSTQKI TRAMQMVAAS KMRRAQERMA QGRPYADNMR RVIAHLVQAN PEYKHRYMVD RPVKRVGYII VSSDRGLAG GLNINLFKKV VQHVKAQQEQ SIEVQFALIG QKAVSFFKNY GGKVLGATTQ IGDAPSLEQL TGSVQVMLDA F DKGELDRI ...String:
MANLKEIRAK VASIKSTQKI TRAMQMVAAS KMRRAQERMA QGRPYADNMR RVIAHLVQAN PEYKHRYMVD RPVKRVGYII VSSDRGLAG GLNINLFKKV VQHVKAQQEQ SIEVQFALIG QKAVSFFKNY GGKVLGATTQ IGDAPSLEQL TGSVQVMLDA F DKGELDRI YLVSNGFVNA MTQKPKVEQL VPLAPAEEGD DLNRTYGWDY IYEPEAEELL NGLLVRYIES MVYQGVIENV AC EQSARMV AMKAATDNAG QLIKDLQLIY NKLRQAAITQ EISEIVGGAA AV

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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

Concentration0.05 mg/mL
BufferpH: 6.8
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
150.0 mMKClPotassium Chloride
2.0 mMMgCl2`Magnesium Chloride
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 300.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: 4ul sample, blotted for 4s at a blotforce of -4..
DetailsSample was applied directly from gel filtration to ultra-thin carbon in peptidiscs.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 85000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsData collected at Diamond Light Source (Harwell, UK) using Titan Krios G3 and automated alignments using Sherpa. Detector used was Gatan K3 including energy filter.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 11490 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 349160
CTF correctionSoftware - Name: cryoSPARC (ver. 2.15)
Startup modelType of model: INSILICO MODEL / Details: Ab initio model generation in CryoSPARC v2.15
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationNumber classes: 3 / Avg.num./class: 33250 / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 25428

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