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- EMDB-48241: Motor domain alone with Apo AAA1 and ADP AAA3 from yeast full-len... -

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Basic information

Entry
Database: EMDB / ID: EMD-48241
TitleMotor domain alone with Apo AAA1 and ADP AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition
Map dataSharpened map of motor domain from yeast full-length dynein-1 with Pac1 in 0.1 mM ATP condition, class-1, Apo AAA1, ADP AAA3
Sample
  • Complex: motor domain alone from yeast full-length dynein-1 complex with Pac1 in 0.1 mM ATP condition
    • Protein or peptide: Dynein heavy chain, cytoplasmic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsdynein / MOTOR PROTEIN
Function / homology
Function and homology information


karyogamy / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / dynein intermediate chain binding ...karyogamy / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / dynein intermediate chain binding / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 ...: / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGeohring IC / Chai P / Iyer BR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142959 United States
CitationJournal: To Be Published
Title: A nucleotide code governs Lis1's ability to relieve dynein autoinhibition
Authors: Geohring IC / Chai P / Iyer BR
History
DepositionDec 10, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48241.png

Downloads & links

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Map

FileDownload / File: emd_48241.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of motor domain from yeast full-length dynein-1 with Pac1 in 0.1 mM ATP condition, class-1, Apo AAA1, ADP AAA3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 384 pix.
= 444.403 Å		1.16 Å/pix.
x 384 pix.
= 444.403 Å		1.16 Å/pix.
x 384 pix.
= 444.403 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1338047 - 1.7085941
Average (Standard dev.)-0.00013028695 (±0.035481554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 444.4032 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48241_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: raw map of motor domain from yeast full-length...

Fileemd_48241_additional_1.map
Annotationraw map of motor domain from yeast full-length dynein-1 with Pac1 in 0.1 mM ATP condition, class-1, Apo AAA1, ADP AAA3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half

Fileemd_48241_half_map_1.map
Annotationhalf
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half

Fileemd_48241_half_map_2.map
Annotationhalf
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : motor domain alone from yeast full-length dynein-1 complex with P...

EntireName: motor domain alone from yeast full-length dynein-1 complex with Pac1 in 0.1 mM ATP condition
Components
  • Complex: motor domain alone from yeast full-length dynein-1 complex with Pac1 in 0.1 mM ATP condition
    • Protein or peptide: Dynein heavy chain, cytoplasmic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: motor domain alone from yeast full-length dynein-1 complex with P...

SupramoleculeName: motor domain alone from yeast full-length dynein-1 complex with Pac1 in 0.1 mM ATP condition
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: class1, Apo AAA1, ADP AAA3, no Pac1 bound
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: Dynein heavy chain, cytoplasmic

MacromoleculeName: Dynein heavy chain, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 471.91875 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MCKNEARLAN ELIEFVAATV TGIKNSPKEN EQAFIDYLHC QYLERFQFFL GLLDGREFDT LFVFLFEELD RTIVTIDIGE EAIYDANLA NKKYSTLLII KSRSVIVDAE PIATQISAIY LPGPVNAGNL ASIITHGVSS VFGQLIKSDT KTYSVETIDK T RRKLDDIS ...String:
MCKNEARLAN ELIEFVAATV TGIKNSPKEN EQAFIDYLHC QYLERFQFFL GLLDGREFDT LFVFLFEELD RTIVTIDIGE EAIYDANLA NKKYSTLLII KSRSVIVDAE PIATQISAIY LPGPVNAGNL ASIITHGVSS VFGQLIKSDT KTYSVETIDK T RRKLDDIS KQFQQLHTSI ETPDLLAMVP SIIKLAVSKG ATSHDYANYL PSNDLESMRF LNILQSIANK WFLVLKQTLA ID RDIKNGS FLDEVEFWSN FYEVLKSLIE QTQSQEFQVC LSVLTNAKRF HNLTNLLNEG SLSDKFKLAD KYNQFLSSIP IDE VRQASN LEDLQELFPV LASSLKKFRY SGYPVQRFVV LMDKISQEVM DAILSNLSDL FQLEYGSFLG LYEKSAGMIE EWDD IVQDV NLLIREDLRK RAPQELLIQK LTFTSASVKA TLDEILSTRK RFFSLAETIK SISPSTYHEE IQRLYHPFEQ IHDIS VNFR LKLEQAESEF SKNMLDLEKK LQNTLASFMD SDHCPTEKLS YLVKFKPLME LCPRIKVKVL ENQQILLLEI KKDIRQ LET GLELLPKILH VEALNNIPPI SARISYFLNV QSRIDNIVQY LEALFGSNWN DTLEGRSIST SIVQLRKETN PHDVFLH WL GNFPEKATAN LLTTPILKLI RNNEDDYELK VNFDFALAAA YSELRSLTYM AFQVPSHIVR IARTYMYLYP RAINLVEL I QTFFSLSKSL SYTFYTNIFL KRNVQTVWLL LQQILITPWE SLQEESSEMS CSVHSLARLE KSIDGILSDY QILKNSEPQ FAKEFSGLKS FDGTADDLHE VEEIISNIQA IFENLFTKGL TNVSDHISTF NNLIISIILE KVRLNLKKMH FPKHVLKLSF NEGRITSSP SLAAMKRSLL KDIEALLNKV VLINFLHDPD HPLSTTLTFN SLVIKLKDDI QNCIEQVQNL HCKINSYVKE W QKMEFLWQ ITEEAFLEVV DNSTQRCFGI LKGLLDSQSK FDLIISRNNF SKNLVLHTED AQRHIRSKMD SWILYVSKHL LT IYERDAR KLHEDMNRDR EAVEDMDINF TSLKNITVII EAVNVNKRHL TERDIQIKLL GSVMRALTKL KVRFPSHFVY IDQ LDNDFS SLRQSLSYVE QELQKHRVVI AKSLEEGVEN INNLSQSLNE SWSVRKPISP TLTPPEALKI LEFFNESITK LKKK MHSVA AAAKMLLIPV VLNDQLTHVV EEVKTYDLVW RSIKNLWEDV QRTFETPWCR VDVLLLQSDL ANFLRRADEL PRAVK QFEM YKSLFSQVNM LTSVNKILVE LKDGALKPRH WNMIFRDIGK RQIQKNLLDK LEFSLKDVMV LNLTLNEILL TKIIER AQK EFVIEKSLNR IKKFWKEAQY EVIEHSSGLK LVREWDVLEQ ACKEDLEELV SMKASNYYKI FEQDCLDLES KLTKLSE IQ VNWVEVQFYW LDLYGILGEN LDIQNFLPLE TSKFKSLTSE YKMITTRAFQ LDTTIEVIHI PNFDTTLKLT IDSLKMIK S SLSTFLERQR RQFPRFYFLG NDDLLKIIGS GKHHDQVSKF MKKMFGSIES IIFLEDFITG VRSVEGEVLN LNEKIELKD SIQAQEWLNI LDTEIKLSVF TQFRDCLGQL KDGTDIEVVV SKYIFQAILL SAQVMWTELV EKCLQTNQFS KYWKEVDMKI KGLLDKLNK SSDNVKKKIE ALLVEYLHFN NVIGQLKNCS TKEEARLLWA KVQKFYQKND TLDDLNSVFI SQSGYLLQYK F EYIGIPER LIYTPLLLIG FATLTDSLHQ KYGGCFFGPA GTGKTETVKA FGQNLGRVVV VFNCDDSFDY QVLSRLLVGI TQ IGAWGCF DEFNRLDEKV LSAVSANIQQ IQNGLQVGKS HITLLEEETP LSPHTAVFIT LNPGYNGRSE LPENLKKSFR EFS MKSPQS GTIAEMILQI MGFEDSKSLA SKIVHFLELL SSKCSSMNHY HFGLRTLKGV LRNCSPLISE FGEGEKTVVE SLKR VILPS LGDTDELVFK DELSKIFDSA GTPLNSKAIV QCLKDAGQRS GFSMSEEFLK KCMQFYYMQK TQQALILVGK AGCGK TATW KTVIDAMAIF DGHANVVYVI DTKVLTKESL YGSMLKATLE WRDGLFTSIL RRVNDDITGT FKNSRIWVVF DSDLDP EYV EAMNSVLDDN KILTLPNGER LPIPPNFRIL FETDNLDHTT PATITRCGLL WFSTDVCSIS SKIDHLLNKS YEALDNK LS MFELDKLKDL ISDSFDMASL TNIFTCSNDL VHILGVRTFN KLETAVQLAV HLISSYRQWF QNLDDKSLKD VITLLIKR S LLYALAGDST GESQRAFIQT INTYFGHDSQ ELSDYSTIVI ANDKLSFSSF CSEIPSVSLE AHEVMRPDIV IPTIDTIKH EKIFYDLLNS KRGIILCGPP GSGKTMIMNN ALRNSSLYDV VGINFSKDTT TEHILSALHR HTNYVTTSKG LTLLPKSDIK NLVLFCDEI NLPKLDKYGS QNVVLFLRQL MEKQGFWKTP ENKWVTIERI HIVGACNPPT DPGRIPMSER FTRHAAILYL G YPSGKSLS QIYEIYYKAI FKLVPEFRSY TEPFARASVH LYNECKARYS TGLQSHYLFS PRELTRLVRG VYTAINTGPR QT LRSLIRL WAYEAWRIFA DRLVGVKEKN SFEQLLYETV DKYLPNQDLG NISSTSLLFS GLLSLDFKEV NKTDLVNFIE ERF KTFCDE ELEVPMVIHE SMVDHILRID RALKQVQGHM MLIGASRTGK TILTRFVAWL NGLKIVQPKI HRHSNLSDFD MILK KAISD CSLKESRTCL IIDESNILET AFLERMNTLL ANADIPDLFQ GEEYDKLLNN LRNKTRSLGL LLDTEQELYD WFVGE IAKN LHVVFTICDP TNNKSSAMIS SPALFNRCII NWMGDWDTKT MSQVANNMVD VIPMEFTDFI VPEVNKELVF TEPIQT IRD AVVNILIHFD RNFYQKMKVG VNPRSPGYFI DGLRALVKLV TAKYQDLQEN QRFVNVGLEK LNESVLKVNE LNKTLSK KS TELTEKEKEA RSTLDKMLME QNESERKQEA TEEIKKILKV QEEDIRKRKE VVMKSIQDIE PTILEAQRGV KNIKKQQL T EIRSMVNPPS GVKIVMEAVC AILGYQFSNW RDIQQFIRKD DFIHNIVHYD TTLHMKPQIR KYMEEEFLSD PNFTYETIN RASKACGPLY QWVNAQINFS KVLENVDPLR QEMKRIEFES LKTKANLLAA EEMTQDLEAS IEVSKRKYSL LIRDVEAIKT EMSNVQANL DRSISLVKSL TFEKERWLNT TKQFSKTSQE LIGNCIISSI YETYFGHLNE RERADMLVIL KRLLGKFAVK Y DVNYRFID YLVTLDEKMK WLECGLDKND YFLENMSIVM NSQDAVPFLL DPSSHMITVI SNYYGNKTVL LSFLEEGFVK RL ENAIRFG SVVIIQDGEF FDPIISRLIS REFNHAGNRV TVEIGDHEVD VSGDFKLFIH SCDPSGDIPI FLRSRVRLVH FVT NKESIE TRIFDITLTE ENAEMQRKRE DLIKLNTEYK LKLKNLEKRL LEELNNSQGN MLENDELMVT LNNLKKEAMN IEKK LSESE EFFPQFDNLV EEYSIIGKHS VKIFSMLEKF GQFHWFYGIS IGQFLSCFKR VFIKKSRETR AARTRVDEIL WLLYQ EVYC QFSTALDKKF KMIMAMTMFC LYKFDIESEQ YKEAVLTMIG VLSESSDGVP KLTVDTNNDL RYLWDYVTTK SYISAL NWF KNEFFVDEWN IADVVANSEN NYFTMASERD VDGTFKLIEL AKASKESLKI IPLGSIENLN YAQEEISKSK IEGGWIL LQ NIQMSLSWVK TYLHKHVEET KAAEEHEKFK MFMTCHLTGD KLPAPLLQRT DRFVYEDIPG ILDTVKDLWG SQFFTGKI S GVWSVYCTFL LSWFHALITA RTRLVPHGFS KKYYFNDCDF QFASVYLENV LATNSTNNIP WAQVRDHIAT IVYGGKIDE EKDLEVVAKL CAHVFCGSDN LQIVPGVRIP QPLLQQSEEE ERARLTAILS NTIEPADSLS SWLQLPRESI LNYERLQAKE VASSTEQLL QEM

UniProtKB: Dynein heavy chain, cytoplasmic

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 45000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 93983
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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