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- EMDB-81338: Dictyostelium discoideum cytoplasmic dynein motor domain in the a... -

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Basic information

Entry
Database: EMDB / ID: EMD-81338
TitleDictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 2)
Map dataPrimary map: Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 2)
Sample
  • Complex: Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the absence of nucleotide
    • Protein or peptide: Dynein heavy chain, cytoplasmic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsdynein / ATPase / motor protein / AAA+ protein
Function / homology
Function and homology information


minus-end-directed vesicle transport along microtubule / early phagosome membrane / Aggrephagy / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / ATPase complex / minus-end-directed microtubule motor activity ...minus-end-directed vesicle transport along microtubule / early phagosome membrane / Aggrephagy / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / ATPase complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / microtubule motor activity / dynein intermediate chain binding / mitotic spindle assembly / endocytic vesicle / cytoplasmic microtubule / cytoplasmic microtubule organization / mitotic spindle organization / tubulin binding / cell cortex / microtubule binding / microtubule / centrosome / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal 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, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal 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 speciesDictyostelium discoideum AX2 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsShimo-Kon R / Tokita H / Imai H / Maeshima T / Kon T
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16K07327 Japan
Japan Society for the Promotion of Science (JSPS)JP21K06096 Japan
Japan Society for the Promotion of Science (JSPS)JP24K09395 Japan
Japan Society for the Promotion of Science (JSPS)JP17H03665 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02259 Japan
Japan Society for the Promotion of Science (JSPS)JP23H02445 Japan
CitationJournal: J Mol Biol / Year: 2026
Title: ADP-Bound States of Cytoplasmic Dynein: Cryo-electron Microscopy Reveals a Two-Step Post-Power-Stroke Transition and Roles of Regulatory ATPase Sites.
Authors: Hiroshi Imai / Riko Kanazawa / Toshihisa Maeshima / Duy Phuoc Tran / Rieko Shimo-Kon / Hisaya Tokita / Tomoko Miyata / Fumiaki Makino / Junso Fujita / Takayuki Kato / Akio Kitao / Keiichi Namba / Takahide Kon /
Abstract: Cytoplasmic dynein is essential for intracellular transport and cell division, and its dysfunction is implicated in severe neurological disorders. Its motility is driven by the primary ATPase site in ...Cytoplasmic dynein is essential for intracellular transport and cell division, and its dysfunction is implicated in severe neurological disorders. Its motility is driven by the primary ATPase site in the AAA1 module and allosterically modulated by regulatory ATPase sites in the AAA3 and AAA4 modules. Despite recent structural advances, post-force-generating (post-power-stroke) transitions and the structural basis of AAA3/AAA4-mediated regulation remain elusive. Using cryo-electron microscopy, we captured intermediate structures of Dictyostelium discoideum cytoplasmic dynein. We identified two distinct ADP-bound states and two apo states, the latter comprising a partially nucleotide-free state with ADP retained at the AAA3 and AAA4 ATPase sites and a fully nucleotide-free state. For the AAA1 ATPase site, our structures and molecular dynamics simulations suggest a dynamic equilibrium between two ADP-bound states. In this model, linker swing and docking onto the AAA5 module can be driven by thermal fluctuations while ADP remains bound at the AAA1 ATPase site, shifting the motor from a canonical ADP-bound state to a metastable apo-like conformation with reduced ADP affinity. This transition could provide a framework for tension-sensing coordination. For the AAA3 and AAA4 ATPase sites, comparison of the partially and fully nucleotide-free apo structures indicates that ADP release induces localized outward tilting of the corresponding large submodules. We propose that this rearrangement displaces the AAA4 Pre-Sensor-I insert from the linker, thereby disfavoring the recovery stroke and stabilizing an inactive state. Together, our findings provide a mechanistic model in which coordinated conformational dynamics across multiple ATPase sites govern dynein's chemomechanical cycle.
History
DepositionJun 9, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_81338.png

Downloads & links

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Map

FileDownload / File: emd_81338.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map: Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261.9 Å		0.87 Å/pix.
x 300 pix.
= 261.9 Å		0.87 Å/pix.
x 300 pix.
= 261.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.873 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-1.549501 - 2.6059544
Average (Standard dev.)0.0017169681 (±0.053187624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B: Dictyostelium discoideum cytoplasmic dynein motor...

Fileemd_81338_half_map_1.map
AnnotationHalf map B: Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A: Dictyostelium discoideum cytoplasmic dynein motor...

Fileemd_81338_half_map_2.map
AnnotationHalf map A: Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 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 : Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in...

EntireName: Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the absence of nucleotide
Components
  • Complex: Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the absence of nucleotide
    • Protein or peptide: Dynein heavy chain, cytoplasmic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in...

SupramoleculeName: Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the absence of nucleotide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Recombinantly expressed and purified HF380 was prepared under nucleotide-free conditions before vitrification.
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)

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Macromolecule #1: Dynein heavy chain, cytoplasmic

MacromoleculeName: Dynein heavy chain, cytoplasmic / type: protein_or_peptide / ID: 1
Details: N-terminal His6-FLAG-tagged HF380 motor-domain construct of Dictyostelium discoideum cytoplasmic dynein heavy chain.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)
Molecular weightTheoretical: 384.331344 KDa
Recombinant expressionOrganism: Dictyostelium discoideum AX2 (eukaryote)
SequenceString: MTRHHHHHHG GGDYKDDDDK GGGKVPVEEE IQDLKAVWVE LSNTWQEIDS LKETAWSAII PRKVRKSLED TLQKLKNLPN RIRQYSAFD HAQNLIKIYL KGNAIITDLH SEAIKDRHWK ILKKRLNTNW IITELTLGSI WDSDLARNEN IYREVITAAQ G EIALEEFL ...String:
MTRHHHHHHG GGDYKDDDDK GGGKVPVEEE IQDLKAVWVE LSNTWQEIDS LKETAWSAII PRKVRKSLED TLQKLKNLPN RIRQYSAFD HAQNLIKIYL KGNAIITDLH SEAIKDRHWK ILKKRLNTNW IITELTLGSI WDSDLARNEN IYREVITAAQ G EIALEEFL KGVREFWTTL ELDLVNYQRK CKLVRGWDDL FNKLAEHLNS ISAMKMSPYY KVFEEEANHW DDRLNKVRSL LD VWIDVQR RWVYLEGIFS GSGDINQLLP AESTRFKSIN SEFIAILKKV SGAPLILEVL AIERIQQTME RLSDLLGKVQ KAL GEYLER QRSAFARFYF VGDEDLLEII GNSKDIIKIQ KHFRKMFAGL ANLTLDDEKT TIIGMSSAEG ETVTFKKPIS IANG PKIHE WLTMVESEMK STLATLLSES LQHFNQVDVN DHSKYSEWVD NYPTQLVLLT SQIVWSTQVD QALGGGTLQQ SKIQE QLQS IEQTTQMILN NLADSVLQDL SAQKRKKFEH LITELVHQRD VVRQLQKCKN LTGNKDFDWL YHMRYYYDAT QENVLH KLV IHMANATFYY GFEYLGIGER LVQTPLTDRC YLTLTQALES RMGGNPFGPA GTGKTETVKA LGSQLGRFVL VFCCDEG FD LQAMSRIFVG LCQCGAWGCF DEFNRLEERI LSAVSQQIQT IQVALKENSK EVELLGGKNI SLHQDMGIFV TMNPGYAG R SNLPDNLKKL FRSMAMIKPD REMIAQVMLY SQGFKTAEVL AGKIVPLFKL CQEQLSAQSH YDFGLRALKS VLVSAGGIK RKCQPPQLPP ITDAESKTKA DQIYCQYEIG VLLNSINDTM IPKLVADDIP LIQSLLLDVF PGSQLQPIQM DQLRKKIQEI AKQRHLVTK QEWVEKILQL HQILNINHGV MMVGPSGGGK TTSWEVYLEA IEQVDNIKSE AHVMDPKAIT KDQLFGSLDL T TREWTDGL FTATLRRIID NVRGESTKRH WIIFDGDVDP EWVENLNSLL DDNKLLTLPN GERLALPNNV RVMFEVQDLK YA TLATISR CGMVWFSEEI LTTQMIFQNY LDTLSNEPFD PQEKEQQKRN ENAQLQQQQQ TTITSPILTS PPTTSSSSRS TTS TTSMIP AGLKVQKECA AIISQYFEPG GLVHKVLEDA GQRPHIMDFT RLRVLNSFFS LMNRSIVNVI EYNQLHSDFP MSPE NQSNY ITNRLLYSLM WGLGGSMGLV ERENFSKFIQ TIAITPVPAN TIPLLDYSVS IDDANWSLWK NKVPSVEVET HKVAS PDVV IPTVDTTRHV DVLHAWLSEH RPLILCGPPG SGKTMTLTST LRAFPDFEVV SLNFSSATTP ELLLKTFDHH CEYKRT PSG ETVLRPTQLG KWLVVFCDEI NLPSTDKYGT QRVITFIRQM VEKGGFWRTS DHTWIKLDKI QFVGACNPPT DAGRVQL TH RFLRHAPILL VDFPSTSSLT QIYGTFNRAL MKLLPNLRSF ADNLTDAMVE FYSESQKRFT PDIQAHYIYS PRELSRWD R ALLEAIQTMD GCTLEGLVRL WAHEALRLFQ DRLVETEEKE WTDKKIDEVA LKHFPSVNLD ALKRPILYSN WLTKDYQPV NRSDLREYVK ARLKVFYEEE LDVPLVLFNE VLDHILRIDR VFRQPQGHAL LIGVSGGGKS VLSRFVAWMN GLSIYTIKVN NNYKSSDFD DDLRMLLKRA GCKEEKICFI FDESNVLESS FLERMNTLLA GGEVPGLFEG EEFTALMHAC KETAQRNGLI L DSEEELYK YFTSQVRRNL HVVFTMNPAS PDFHNRSATS PALFNRCVLD WFGEWSPEAL FQVGSEFTRN LDLENPQYIA PP VFIQEAE IMGNNLMAIP PSHRDAVVSS LVYIHQTIGE ANIRLLKRQG RQNYVTPRHY LDFINQVVLL INEKRDQLEE EQL HLNIGL KKLRDTEAQV KDLQVSLAQK NRELDVKNEQ ANQKLKQMVQ DQQAAEIKQK DARELQVQLD VRNKEIAVQK VKAY ADLEK AEPAIIEAQE AVSTIKKKHL DEIKSLPKPP TPVKLAMEAV CLMLGGKKLE WADIRKKIME PNFITSIINY DTKKM MTPK IREAITKGYL EDPGFDYETV NRASKACGPL VKWATAQTYY SEILDRIKPL REEVEQLENA ANELKLKQDE IVATIT ALE KSIATYKEEY ATLIRETEQI KTESSKVKNK VDRSIALLDN LNSERGRWEQ QSENFNTQMS TVVGDVVLAS AFLAYIG FF DQNFRTDLMR KWMIRLDSVG IKFKSDLSVP SFLSKPEERL NWHANSLPSD ELCIENAIML KRFNRYPLVI DPSGQAME F LMNQYADKKI TKTSFLDSSF MKNLESALRF GCPLLVQDVE NIDPVLNPVL NKEIRKKGGR ILIRLGDQDV DFSPSFMIF LFTRDPTAHF TPDLCSRVTF VNFTVTPSSL QSQCLHEALK TERPDTHKKR SDLLKIQGEF QVKLRILEKS LLNALSQASG NILDDDSVI STLETLKKET TEIALKVEET ETVMQEISEV SALYNPMALS CSRVYFAMEE LSQFHLYQFS LRAFLDIFYN L LNNNPNLV DKKDPNERLV YLSKDIFSMT FNRVTRTLLN DDKLTFALQL TIISVKGTSN EIEESEWDFL LKGGDNLTSI KE TIPQLDS LLSTTQQKWL ICLRQQVPSF SKLVDHIQQN SSDWKQFFGK DQVGEPIIPE SWIVAQAQLS NQQSTIVSNF RKI LLMKAF HSDRVLQYSH SFVCSVFGED FLNTQELDMA NIVEKEVKSS SPLLLCSVPG YDASSKVDDL ALQLHKQYKS FAIG SPEGF ELAEKSIYAA AKSGTWVLLK NIHLAPQWLV QLEKKLHSLS PHPSFRLFMT SEIHPALPAN LLRMSNVFSY ENPPG VKAN LLHTFIGIPA TRMDKQPAER SRIYFLLAWF HAIIQERLRY IPLGWTKFFE FNDADLRGAL DSIDYWVDLY SKGRSN IDP DKIPWIAVRT ILGSTIYGGR IDNEFDMRLL YSFLEQLFTP SAFNPDFPLV PSIGLSVPEG TTRAHFMKWI EALPEIS TP IWLGLPENAE SLLLSNKARK MINDLQKMQS SEEDGEDDQV SGSSKKESSS SSSEDKGKAK LRATITEWTK LLPKPLKQ L KRTTQNIKDP LFRCFEREIS TGGKLVKKIT NDLANLLELI SGNIKSTNYL RSLTTSISKG IVPKEWKWYS VPETISLSV WISDFSKRMQ QLSEISESSD YSSIQVWLGG LLNPEAYITA TRQSASQLNG WSLENLRLHA SSLGKISSEG GASFNVKGMA LEGAVWNND QLTPTDILST PISIATLTWK DKDDPIFNNS SSKLSVPVYL NETRSELLFS IDLPYDQSTS KQNWYQRSVS I SSWKSDI

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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / 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

Concentration4.0 mg/mL
BufferpH: 7.1
Component:
ConcentrationFormulaName
10.0 mMK-PIPESK-PIPES
4.0 mMMgSO4magnesium sulfate
1.0 mMEGTAEGTA
0.1 % v/vTween-20

Details: 10 mM K-PIPES, 4 mM MgSO4, 1 mM EGTA, 0.1% (v/v) Tween-20, pH 7.1
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
Details: Grids were glow-discharged using a JEC-3000FC sputter coater (JEOL, Japan) at 20 mA for 20 s.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM (ver. 3.8 or 4.050)
Details: Automated data collection using SerialEM in combination with yoneo-Locr version 1.051.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 32531 / Average electron dose: 80.0 e/Å2
Details: Images were collected in movie-mode. Dose rate was 2.0 electrons/angstrom squared/frame.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsMovies were motion-corrected using Patch Motion Correction, and CTF parameters were estimated using Patch CTF estimation in cryoSPARC 4.4.1. Micrographs with CTF-estimated maximum resolutions better than 6 angstrom were retained for further processing.
Particle selectionNumber selected: 1108632
Details: Particles were selected by blob picking and template-based picking in cryoSPARC. Template-picked particles were extracted with a 300-pixel box and cleaned by 2D classification, yielding 1,108,632 particles.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1)
Software - details: Patch CTF estimation; global and local CTF refinement.
Details: CTF parameters were estimated using Patch CTF estimation in cryoSPARC and further refined by global and local CTF refinement.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: An ab initio 3D reconstruction was generated in cryoSPARC from 2D class averages.
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Non-uniform refinement was performed.
Details: The selected particles were refined by non-uniform refinement in cryoSPARC.
Number images used: 910656
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Software - details: Initial orientation assignment during ab initio 3D reconstruction and refinement.
Details: Initial orientations were assigned during ab initio 3D reconstruction in cryoSPARC.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Software - details: Final orientation refinement during non-uniform refinement.
Details: Final orientations were refined during non-uniform refinement in cryoSPARC.
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: 3D classification
Details: The 1,108,632-particle set was subjected to 3D classification into five classes. Particles from four selected classes were combined for final refinement.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3vkg


Chain - Chain ID: A / Chain - Residue range: 1410-4729 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Initial model for the HF380 dynein motor domain.
SoftwareName: UCSF ChimeraX (ver. 1.7)
Details: Rigid-body fitting of the initial model into the cryo-EM map.
DetailsA monomeric HF380 motor-domain model was fitted into the cryo-EM map and refined by phenix.real_space_refine.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 92.3
Target criteria: Real-space target; weighted map sum at atom centers
Output model

PDB-27qb:
Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 2)

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