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- EMDB-10862: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-10862
TitleCryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1/peripheral stalk
Map dataLocal-resolution filtered full map of T. thermophila ATP synthase F1/peripheral stalk
Sample
  • Complex: Mitochondrial ATP synthase, F1/peripheral stalk
    • Protein or peptide: x 8 types
  • Ligand: x 3 types
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / 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 / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / 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, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / 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 / 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 beta / Uncharacterized protein / Transmembrane protein, putative / Uncharacterized protein / ATP synthase F1, delta subunit / ATP synthase subunit gamma / Uncharacterized protein / ATP synthase subunit alpha
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKock Flygaard R / Muhleip A / Amunts A
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
CitationJournal: Nat Commun / Year: 2020
Title: Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Authors: Rasmus Kock Flygaard / Alexander Mühleip / Victor Tobiasson / Alexey Amunts /
Abstract: Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we ...Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.
History
DepositionApr 14, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateNov 11, 2020-
Current statusNov 11, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yo0
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yo0
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10862.png

Downloads & links

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Map

FileDownload / File: emd_10862.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal-resolution filtered full map of T. thermophila ATP synthase F1/peripheral stalk
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.032918505 - 0.091995
Average (Standard dev.)0.00030685085 (±0.002157341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z498.000498.000498.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0330.0920.000

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Supplemental data

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Mask #1

Fileemd_10862_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_10862_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_10862_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial ATP synthase, F1/peripheral stalk

EntireName: Mitochondrial ATP synthase, F1/peripheral stalk
Components
  • Complex: Mitochondrial ATP synthase, F1/peripheral stalk
    • Protein or peptide: Oligomycin sensitivity-conferring protein (OSCP)
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: Inhibitor of F1 (IF1)
    • Protein or peptide: ATPTT13
    • Protein or peptide: subunit b
    • Protein or peptide: subunit d
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Mitochondrial ATP synthase, F1/peripheral stalk

SupramoleculeName: Mitochondrial ATP synthase, F1/peripheral stalk / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: Oligomycin sensitivity-conferring protein (OSCP)

MacromoleculeName: Oligomycin sensitivity-conferring protein (OSCP) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 24.782355 KDa
SequenceString: MQVIRKHLAQ KGLFNPFLFN RFSTQQDITS VPGDKPPAIE DSIHGKYAGV LFSSASSNKS LNKVAEDMKY FNQLYKESEV FKSFLNNVS LKRNQQRDII SALGKTNFNP ATNNLLETLI ENKRLDSLPK IAEKYMDYYR ILNKQESITI ISAQELTAAE K QKVEQGLK ...String:
MQVIRKHLAQ KGLFNPFLFN RFSTQQDITS VPGDKPPAIE DSIHGKYAGV LFSSASSNKS LNKVAEDMKY FNQLYKESEV FKSFLNNVS LKRNQQRDII SALGKTNFNP ATNNLLETLI ENKRLDSLPK IAEKYMDYYR ILNKQESITI ISAQELTAAE K QKVEQGLK KGNANVQFTV VYQVDPAILG GLQMYSGNNF LDCSLLSRVN KLKTEIAKIS F

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Macromolecule #2: ATP synthase subunit gamma

MacromoleculeName: ATP synthase subunit gamma / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 32.915152 KDa
SequenceString: MFGLASKGFI NTSLVMVPQM NFGANLKQLK IRMKAIGSIK KITKAMKMVA ASKMKAETSR LENGRNFAVG SVQKMLENES YVQKKKSTT APKSTLLVPI TSDKGLCGSV NSSIVREVKR LALNNRSAFG LLPVGEKGSS GLSRPFPDLL KSSIVNIQNV N FPTAAAIA ...String:
MFGLASKGFI NTSLVMVPQM NFGANLKQLK IRMKAIGSIK KITKAMKMVA ASKMKAETSR LENGRNFAVG SVQKMLENES YVQKKKSTT APKSTLLVPI TSDKGLCGSV NSSIVREVKR LALNNRSAFG LLPVGEKGSS GLSRPFPDLL KSSIVNIQNV N FPTAAAIA HQVSTQGAGY DQVTLIYNHF KNAISYVVKH QELLPRAQFL NLFKYVTRHE AVEPELEYSK NYFFELYMAS SV YNALLNS SASEQASRMN AMENASKNAG EILSKLTLDY NKARQAKITM ELIEIISGAS IV

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Macromolecule #3: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 59.744012 KDa
SequenceString: MIRNFHSLVK RVPRLALTPF FGFRTSMTLA DKKLSTGEAS VVLAEKIKGI TQQNDITEYG TVISIGDGIA RVFGLTKVQA GEMVEFKSG IRGMALNLET DNVGVVVLGN DRDIKEGDVV KRTGAIVDVP IGEAMCGRVF DALGNPIDGL GPLKTTQRAR V EIKAPGII ...String:
MIRNFHSLVK RVPRLALTPF FGFRTSMTLA DKKLSTGEAS VVLAEKIKGI TQQNDITEYG TVISIGDGIA RVFGLTKVQA GEMVEFKSG IRGMALNLET DNVGVVVLGN DRDIKEGDVV KRTGAIVDVP IGEAMCGRVF DALGNPIDGL GPLKTTQRAR V EIKAPGII PRQSVRQPMQ TGIKCVDSLV PIGRGQRELI IGDRQTGKTA IAIDTILNQK EAFNTGDVKK QLYCIYVAVG QK RSTIANL VSILKQHDCM KFTIVVCATA SDAAPLQFLA PYSGCAIGEF FRDNGKHALI IYDDLSKQAV AYRQMSLLLR RPP GREAYP GDVFYLHSRL LERAAKMNDS LGGGSLTALP VIETQAGDVS AYIPTNVISI TDGQIFLETE LFYKGIRPAI NVGL SVSRV GSAAQIKAMK KIAGNLKLTL ATYRELAAFS QFGSDLDAKT QQQLNTGERL VEMLKQNQYT PMKVEEQVCI IFAGV KGFL DALVTSEVLK FEKKFLEHVR TNHSALLKRI RDSGDLSEVD TNELNTIIPL FIQEGGFKLK AQ

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Macromolecule #4: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 53.490848 KDa
SequenceString: MLSKALQRGI ARAFSTTAKK EAPKTVKANG QVSQVIGAVV DVQFEGELPQ ILNALEVQGT QHRLVLEVAQ HLGDSRVRTI AMDSTEGLV RGQPVVDTGL PISVPVGPGT LGRIMNVIGE PIDQRGPIKA AKLYPIHRDA PSFTDQATSA EILVTGIKVV D LLAPYARG ...String:
MLSKALQRGI ARAFSTTAKK EAPKTVKANG QVSQVIGAVV DVQFEGELPQ ILNALEVQGT QHRLVLEVAQ HLGDSRVRTI AMDSTEGLV RGQPVVDTGL PISVPVGPGT LGRIMNVIGE PIDQRGPIKA AKLYPIHRDA PSFTDQATSA EILVTGIKVV D LLAPYARG GKIGLFGGAG VGKTVLIQEL INNVAKHHGG YSVFAGVGER TREGNDLYHE MMDSKVISVK EGESRCALIF GQ MNEPPGA RARVGLTGLT VAEYFRDEEG KDVLLFVDNI FRFTQACSEV SALLGRIPSA VGYQPTLATD LGALQERITT TQK GSITSV QAIYVPADDL TDPAPATTFA HLDATTVLNR GLTELGIYPA VDPLDSTSRM LDPITIGEEH YTVARGVQKL LQDY KSLQD IIAILGVDDL SEEDKLVVAR ARKVQKFLSQ PFFMSEVFSG IPGRFVNLKQ NIASFKALLE GAGDEYPESC FYMKG DLEE SLAAGRADAL KSK

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Macromolecule #5: Inhibitor of F1 (IF1)

MacromoleculeName: Inhibitor of F1 (IF1) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 12.987691 KDa
SequenceString:
MNRSVNIAKN LIQTYRAMSV QSRFAFSTRE EEWLDKRTKS QEKVYFDQED RKAMKRLLEK LNTTSKFVED SEYLAPQNLE VENILKRYH INYTQALIDE LVDWKTGKN

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Macromolecule #6: ATPTT13

MacromoleculeName: ATPTT13 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 16.81625 KDa
SequenceString:
MNSLSSKKAN SLVFKSIRNF TLQWGSLAER PMVDRVMSTS TWPVPYYQRL FKAYPIREKK DKMSLLLSDI DIDDTNWYQA KDFLRGSFR GRQIVDYVEN NIASNTYILI QQDVANMAKA YVHDICGYID VANKENVRIL SKGDLI

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Macromolecule #7: subunit b

MacromoleculeName: subunit b / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 43.910102 KDa
SequenceString: MHSTLRVFTK NNCLSFTNMN RFSTAAQVAQ ANYSKFRADY SASVAAFQQR IKTIEKENTG SMKKPMAKAY EHPYNSEHHP LNFSAVKIA ETFHDFIGPE QVSPHYESFA MSRKFLLTFW GGFFVLNFGM ATVDLNWIMK STYIPWIFWF QLMYFYVEGK N SMFMPLLQ ...String:
MHSTLRVFTK NNCLSFTNMN RFSTAAQVAQ ANYSKFRADY SASVAAFQQR IKTIEKENTG SMKKPMAKAY EHPYNSEHHP LNFSAVKIA ETFHDFIGPE QVSPHYESFA MSRKFLLTFW GGFFVLNFGM ATVDLNWIMK STYIPWIFWF QLMYFYVEGK N SMFMPLLQ RFYRRAAANE IFTMEAFYHE NIENKLRNLM RITKGQLEYW DIHTSYGEIR ADSINNFLAN EYLRLQSHIT SR ALNILKQ AQAYETMNQA ALLQKLIDDA TSAIDNALKG DKKAEVLARS LDSAIDGLSK GYMDYQNDPL LPLILSSIEA NVK KITTLS AQEQANLIGL TAEQLKSIKE NDVRARKEFL ESQPKLDNNL KNIESVKKIL ATWGK

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Macromolecule #8: subunit d

MacromoleculeName: subunit d / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 26.747951 KDa
SequenceString: MSMLAKIAKN VVKTQALKNT TAAQTPSFQA PGNQDKILKW ISTLSNKATT GESRSYCTQL SSLVSFYNKQ HVEQIPTIDF NEWKSVIST QGLVDKVKEN YESLIKEQYN TDAISKQISS ASSKALDDIE NELSFHAAIW LNAYADYTMF LFELEEYNDP N DYLMHENF ...String:
MSMLAKIAKN VVKTQALKNT TAAQTPSFQA PGNQDKILKW ISTLSNKATT GESRSYCTQL SSLVSFYNKQ HVEQIPTIDF NEWKSVIST QGLVDKVKEN YESLIKEQYN TDAISKQISS ASSKALDDIE NELSFHAAIW LNAYADYTMF LFELEEYNDP N DYLMHENF DFFRGLETEL EELTETHNYI PGAKDDVNLR GYLATQFAWG KKVISFYRHP ADDFKCAKAT KNMLGR

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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: 5 / 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: 2 / 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

Concentration0.75 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: beta
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: beta
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: beta / Number images used: 61157
FSC plot (resolution estimation)

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