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- EMDB-36589: Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-36589
TitleCryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587
Map data
Sample
  • Complex: Mycobacterium tuberculosis ATP synthase
    • Protein or peptide: x 4 types
  • Protein or peptide: x 4 types
  • Ligand: x 4 types
KeywordsATP synthase / Mycobacterium tuberculosis / cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / 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 / peptidoglycan-based cell wall / ADP binding / hydrolase activity ...proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / 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 / peptidoglycan-based cell wall / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytosol
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, F0 complex, subunit C, bacterial/chloroplast / 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, 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, F0 complex, subunit C, bacterial/chloroplast / 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 b / ATP synthase subunit c / ATP synthase subunit a / Multifunctional fusion protein / ATP synthase subunit beta / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase epsilon chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang Y / Lai Y / Liu F / Rao Z / Gong H
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: To Be Published
Title: Structure of Mycobacterium tuberculosis ATP synthase
Authors: Zhang Y / Lai Y / Liu F / Rao Z / Gong H
History
DepositionJun 15, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36589.png

Downloads & links

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Map

FileDownload / File: emd_36589.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.73 Å
Density
Contour LevelBy AUTHOR: 5.6
Minimum - Maximum-27.483136999999999 - 41.550666999999997
Average (Standard dev.)0.01160014 (±1.1070261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mycobacterium tuberculosis ATP synthase

EntireName: Mycobacterium tuberculosis ATP synthase
Components
  • Complex: Mycobacterium tuberculosis ATP synthase
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
  • Protein or peptide: ATP synthase subunit c
  • Protein or peptide: ATP synthase subunit a
  • Protein or peptide: ATP synthase subunit b
  • Protein or peptide: Multifunctional fusion protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol

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Supramolecule #1: Mycobacterium tuberculosis ATP synthase

SupramoleculeName: Mycobacterium tuberculosis ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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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: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 59.35807 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAELTIPADD IQSAIEEYVS SFTADTSREE VGTVVDAGDG IAHVEGLPSV MTQELLEFPG GILGVALNLD EHSVGAVILG DFENIEEGQ QVKRTGEVLS VPVGDGFLGR VVNPLGQPID GRGDVDSDTR RALELQAPSV VHRQGVKEPL QTGIKAIDAM T PIGRGQRQ ...String:
MAELTIPADD IQSAIEEYVS SFTADTSREE VGTVVDAGDG IAHVEGLPSV MTQELLEFPG GILGVALNLD EHSVGAVILG DFENIEEGQ QVKRTGEVLS VPVGDGFLGR VVNPLGQPID GRGDVDSDTR RALELQAPSV VHRQGVKEPL QTGIKAIDAM T PIGRGQRQ LIIGDRKTGK TAVCVDTILN QRQNWESGDP KKQVRCVYVA IGQKGTTIAA VRRTLEEGGA MDYTTIVAAA AS ESAGFKW LAPYTGSAIA QHWMYEGKHV LIIFDDLTKQ AEAYRAISLL LRRPPGREAY PGDVFYLHSR LLERCAKLSD DLG GGSLTG LPIIETKAND ISAYIPTNVI SITDGQCFLE TDLFNQGVRP AINVGVSVSR VGGAAQIKAM KEVAGSLRLD LSQY RELEA FAAFASDLDA ASKAQLERGA RLVELLKQPQ SQPMPVEEQV VSIFLGTGGH LDSVPVEDVR RFETELLDHM RASEE EILT EIRDSQKLTE EAADKLTEVI KNFKKGFAAT GGGSVVPDEH VEALDEDKLA KEAVKVKKPA PKKKK

UniProtKB: ATP synthase subunit alpha

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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: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 53.150934 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTTTAEKTDR PGKPGSSDTS GRVVRVTGPV VDVEFPRGSI PELFNALHAE ITFESLAKTL TLEVAQHLGD NLVRTISLQP TDGLVRGVE VIDTGRSISV PVGEGVKGHV FNALGDCLDE PGYGEKFEHW SIHRKPPAFE ELEPRTEMLE TGLKVVDLLT P YVRGGKIA ...String:
MTTTAEKTDR PGKPGSSDTS GRVVRVTGPV VDVEFPRGSI PELFNALHAE ITFESLAKTL TLEVAQHLGD NLVRTISLQP TDGLVRGVE VIDTGRSISV PVGEGVKGHV FNALGDCLDE PGYGEKFEHW SIHRKPPAFE ELEPRTEMLE TGLKVVDLLT P YVRGGKIA LFGGAGVGKT VLIQEMINRI ARNFGGTSVF AGVGERTREG NDLWVELAEA NVLKDTALVF GQMDEPPGTR MR VALSALT MAEWFRDEQG QDVLLFIDNI FRFTQAGSEV STLLGRMPSA VGYQPTLADE MGELQERITS TRGRSITSMQ AVY VPADDY TDPAPATTFA HLDATTELSR AVFSKGIFPA VDPLASSSTI LDPSVVGDEH YRVAQEVIRI LQRYKDLQDI IAIL GIDEL SEEDKQLVNR ARRIERFLSQ NMMAAEQFTG QPGSTVPVKE TIEAFDRLCK GDFDHVPEQA FFLIGGLDDL AKKAE SLGA KL

UniProtKB: ATP synthase subunit beta

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Macromolecule #3: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 33.929332 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIARAQARL ESARPYAFEI TRMLTTLAAE AALDHPLLVE RPEPKRAGVL VVSSDRGLC GAYNANIFRR SEELFSLLRE AGKQPVLYVV GRKAQNYYSF RNWNITESWM GFSEQPTYEN AAEIASTLVD A FLLGTDNG ...String:
MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIARAQARL ESARPYAFEI TRMLTTLAAE AALDHPLLVE RPEPKRAGVL VVSSDRGLC GAYNANIFRR SEELFSLLRE AGKQPVLYVV GRKAQNYYSF RNWNITESWM GFSEQPTYEN AAEIASTLVD A FLLGTDNG EDQRSDSGEG VDELHIVYTE FKSMLSQSAE AHRIAPMVVE YVEEDIGPRT LYSFEPDATM LFESLLPRYL TT RVYAALL ESAASELASR QRAMKSATDN ADDLIKALTL MANRERQAQI TQEISEIVGG ANALAEAR

UniProtKB: ATP synthase gamma chain

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Macromolecule #4: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.149744 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MAELNVEIVA VDRNIWSGTA KFLFTRTTVG EIGILPRHIP LVAQLVDDAM VRVEREGEKD LRIAVDGGFL SVTEEGVSIL AESAEFESE IDEAAAKQDS ESDDPRIAAR GRARLRAVGA ID

UniProtKB: ATP synthase epsilon chain

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Macromolecule #5: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 5 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.058423 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MDPTIAAGAL IGGGLIMAGG AIGAGIGDGV AGNALISGVA RQPEAQGRLF TPFFITVGLV EAAYFINLAF MALFVFATPV K

UniProtKB: ATP synthase subunit c

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Macromolecule #6: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 27.488436 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL ...String:
MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL APINLVEEVA KPISLSLRLF GNIFAGGILV ALIALFPPYI MWAPNAIWKA FDLFVGAIQA FIFALLTILY FS QAMELEE EHH

UniProtKB: ATP synthase subunit a

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Macromolecule #7: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 18.345771 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MGEVSAIVLA ASQAAEEGGE SSNFLIPNGT FFVVLAIFLV VLAVIGTFVV PPILKVLRER DAMVAKTLAD NKKSDEQFAA AQADYDEAM TEARVQASSL RDNARADGRK VIEDARVRAE QQVASTLQTA HEQLKRERDA VELDLRAHVG TMSATLASRI L GVDLTASA ATR

UniProtKB: ATP synthase subunit b

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Macromolecule #8: Multifunctional fusion protein

MacromoleculeName: Multifunctional fusion protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 48.866648 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MSTFIGQLFG FAVIVYLVWR FIVPLVGRLM SARQDTVRQQ LADAAAAADR LAEASQAHTK ALEDAKSEAH RVVEEARTDA ERIAEQLEA QADVEAERIK MQGARQVDLI RAQLTRQLRL ELGHESVRQA RELVRNHVAD QAQQSATVDR FLDQLDAMAP A TADVDYPL ...String:
MSTFIGQLFG FAVIVYLVWR FIVPLVGRLM SARQDTVRQQ LADAAAAADR LAEASQAHTK ALEDAKSEAH RVVEEARTDA ERIAEQLEA QADVEAERIK MQGARQVDLI RAQLTRQLRL ELGHESVRQA RELVRNHVAD QAQQSATVDR FLDQLDAMAP A TADVDYPL LAKMRSASRR ALTSLVDWFG TMAQDLDHQG LTTLAGELVS VARLLDREAV VTRYLTVPAE DATPRIRLIE RL VSGKVGA PTLEVLRTAV SKRWSANSDL IDAIEHVSRQ ALLELAERAG QVDEVEDQLF RFSRILDVQP RLAILLGDCA VPA EGRVRL LRKVLERADS TVNPVVVALL SHTVELLRGQ AVEEAVLFLA EVAVARRGEI VAQVGAAAEL SDAQRTRLTE VLSR IYGHP VTVQLHIDAA LLGGLSIAVG DEVIDGTLSS RLAAAEARLP D

UniProtKB: Multifunctional fusion protein

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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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Macromolecule #12: (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimet...

MacromoleculeName: (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol
type: ligand / ID: 12 / Number of copies: 7 / Formula: UTI
Molecular weightTheoretical: 614.503 Da

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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 defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81528

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