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- EMDB-47371: Cryo-EM structure of human cytoplasmic dynein-1 in the presence of ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-47371
TitleCryo-EM structure of human cytoplasmic dynein-1 in the presence of ATP
Map data
Sample
  • Complex: Human Cytoplasmic dynein-1 bound to LIS1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsHuman / MOTOR PROTEIN
Function / homology
Function and homology information


positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / minus-end-directed microtubule motor activity / P-body assembly / dynein light intermediate chain binding ...positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / minus-end-directed microtubule motor activity / P-body assembly / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration / cytoplasmic microtubule / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / stress granule assembly / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic spindle organization / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / HCMV Early Events / Aggrephagy / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytosol
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 / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 ...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 / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / 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
Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNguyen KHV / Kendrick AA / Leschziner AE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM139795 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM145296 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Pre-Chi dynein bound to Lis1
Authors: Nguyen KHV / Kendrick AA / Leschziner AE
History
DepositionOct 19, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47371.png

Downloads & links

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Map

FileDownload / File: emd_47371.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 352 pix.
= 329.12 Å		0.94 Å/pix.
x 352 pix.
= 329.12 Å		0.94 Å/pix.
x 352 pix.
= 329.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.3326647 - 0.6361945
Average (Standard dev.)0.00023995595 (±0.0223958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 329.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47371_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47371_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human Cytoplasmic dynein-1 bound to LIS1

EntireName: Human Cytoplasmic dynein-1 bound to LIS1
Components
  • Complex: Human Cytoplasmic dynein-1 bound to LIS1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human Cytoplasmic dynein-1 bound to LIS1

SupramoleculeName: Human Cytoplasmic dynein-1 bound to LIS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1

MacromoleculeName: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 554.12625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GDYDIPTTEN LYFQGDKDCE MKRTTLDSPL GKLELSGCEQ GLHRIIFLGK GTSAADAVEV PAPAAVLGGP EPLMQATAWL NAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYS HLAALAGNPA ATAAVKTALS GNPVPILIPC H RVVQGDLD ...String:
GDYDIPTTEN LYFQGDKDCE MKRTTLDSPL GKLELSGCEQ GLHRIIFLGK GTSAADAVEV PAPAAVLGGP EPLMQATAWL NAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYS HLAALAGNPA ATAAVKTALS GNPVPILIPC H RVVQGDLD VGGYEGGLAV KEWLLAHEGH RLGKPGLGGS SEPGGGGGED GSAGLEVSAV QNVADVSVLQ KHLRKLVPLL LE DGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVGD EGEEEKEFIS YNINIDIHYG VKSNSLAFIK RTP VIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP FFKSYIRESG KADRDGDKMA PSVEKKIAEL EMGLLHLQQN IEIP EISLP IHPMITNVAK QCYERGEKPK VTDFGDKVED PTFLNQLQSG VNRWIREIQK VTKLDRDPAS GTALQEISFW LNLER ALYR IQEKRESPEV LLTLDILKHG KRFHATVSFD TDTGLKQALE TVNDYNPLMK DFPLNDLLSA TELDKIRQAL VAIFTH LRK IRNTKYPIQR ALRLVEAISR DLSSQLLKVL GTRKLMHVAY EEFEKVMVAC FEVFQTWDDE YEKLQVLLRD IVKRKRE EN LKMVWRINPA HRKLQARLDQ MRKFRRQHEQ LRAVIVRVLR PQVTAVAQQN QGEVPEPQDM KVAEVLFDAA DANAIEEV N LAYENVKEVD GLDVSKEGTE AWEAAMKRYD ERIDRVETRI TARLRDQLGT AKNANEMFRI FSRFNALFVR PHIRGAIRE YQTQLIQRVK DDIESLHDKF KVQYPQSQAC KMSHVRDLPP VSGSIIWAKQ IDRQLTAYMK RVEDVLGKGW ENHVEGQKLK QDGDSFRMK LNTQEIFDDW ARKVQQRNLG VSGRIFTIES TRVRGRTGNV LKLKVNFLPE IITLSKEVRN LKWLGFRVPL A IVNKAHQA NQLYPFAISL IESVRTYERT CEKVEERNTI SLLVAGLKKE VQALIAEGIA LVWESYKLDP YVQRLAETVF NF QEKVDDL LIIEEKIDLE VRSLETCMYD HKTFSEILNR VQKAVDDLNL HSYSNLPIWV NKLDMEIERI LGVRLQAGLR AWT QVLLGQ AEDKAEVDMD TDAPQVSHKP GGEPKIKNVV HELRITNQVI YLNPPIEECR YKLYQEMFAW KMVVLSLPRI QSQR YQVGV HYELTEEEKF YRNALTRMPD GPVALEESYS AVMGIVSEVE QYVKVWLQYQ CLWDMQAENI YNRLGEDLNK WQALL VQIR KARGTFDNAE TKKEFGPVVI DYGKVQSKVN LKYDSWHKEV LSKFGQMLGS NMTEFHSQIS KSRQELEQHS VDTAST SDA VTFITYVQSL KRKIKQFEKQ VELYRNGQRL LEKQRFQFPP SWLYIDNIEG EWGAFNDIMR RKDSAIQQQV ANLQMKI VQ EDRAVESRTT DLLTDWEKTK PVTGNLRPEE ALQALTIYEG KFGRLKDDRE KCAKAKEALE LTDTGLLSGS EERVQVAL E ELQDLKGVWS ELSKVWEQID QMKEQPWVSV QPRKLRQNLD ALLNQLKSFP ARLRQYASYE FVQRLLKGYM KINMLVIEL KSEALKDRHW KQLMKRLHVN WVVSELTLGQ IWDVDLQKNE AIVKDVLLVA QGEMALEEFL KQIREVWNTY ELDLVNYQNK CRLIRGWDD LFNKVKEHIN SVSAMKLSPY YKVFEEDALS WEDKLNRIMA LFDVWIDVQR RWVYLEGIFT GSADIKHLLP V ETQRFQSI STEFLALMKK VSKSPLVMDV LNIQGVQRSL ERLADLLGKI QKALGEYLER ERSSFPRFYF VGDEDLLEII GN SKNVAKL QKHFKKMFAG VSSIILNEDN SVVLGISSRE GEEVMFKTPV SITEHPKINE WLTLVEKEMR VTLAKLLAES VTE VEIFGK ATSIDPNTYI TWIDKYQAQL VVLSAQIAWS ENVETALSSM GGGGDAAPLH SVLSNVEVTL NVLADSVLME QPPL RRRKL EHLITELVHQ RDVTRSLIKS KIDNAKSFEW LSQMRFYFDP KQTDVLQQLS IQMANAKFNY GFEYLGVQDK LVQTP LTDR CYLTMTQALE ARLGGSPFGP AGTGKTESVK ALGHQLGRFV LVFNCDETFD FQAMGRIFVG LCQVGAWGCF DEFNRL EER MLSAVSQQVQ CIQEALREHS NPNYDKTSAP ITCELLNKQV KVSPDMAIFI TMNPGYAGRS NLPDNLKKLF RSLAMTK PD RQLIAQVMLY SQGFRTAEVL ANKIVPFFKL CDEQLSSQSH YDFGLRALKS VLVSAGNVKR ERIQKIKREK EERGEAVD E GEIAENLPEQ EILIQSVCET MVPKLVAEDI PLLFSLLSDV FPGVQYHRGE MTALREELKK VCQEMYLTYG DGEEVGGMW VEKVLQLYQI TQINHGLMMV GPSGSGKSMA WRVLLKALER LEGVEGVAHI IDPKAISKDH LYGTLDPNTR EWTDGLFTHV LRKIIDSVR GELQKRQWIV FDGDVDPEWV ENLNSVLDDN KLLTLPNGER LSLPPNVRIM FEVQDLKYAT LATVSRCGMV W FSEDVLST DMIFNNFLAR LRSIPLDEGE DEAQRRRKGK EDEGEEAASP MLQIQRDAAT IMQPYFTSNG LVTKALEHAF QL EHIMDLT RLRCLGSLFS MLHQACRNVA QYNANHPDFP MQIEQLERYI QRYLVYAILW SLSGDSRLKM RAELGEYIRR ITT VPLPTA PNIPIIDYEV SISGEWSPWQ AKVPQIEVET HKVAAPDVVV PTLDTVRHEA LLYTWLAEHK PLVLCGPPGS GKTM TLFSA LRALPDMEVV GLNFSSATTP ELLLKTFDHY CEYRRTPNGV VLAPVQLGKW LVLFCDEINL PDMDKYGTQR VISFI RQMV EHGGFYRTSD QTWVKLERIQ FVGACNPPTD PGRKPLSHRF LRHVPVVYVD YPGPASLTQI YGTFNRAMLR LIPSLR TYA EPLTAAMVEF YTMSQERFTQ DTQPHYIYSP REMTRWVRGI FEALRPLETL PVEGLIRIWA HEALRLFQDR LVEDEER RW TDENIDTVAL KHFPNIDREK AMSRPILYSN WLSKDYIPVD QEELRDYVKA RLKVFYEEEL DVPLVLFNEV LDHVLRID R IFRQPQGHLL LIGVSGAGKT TLSRFVAWMN GLSVYQIKVH RKYTGEDFDE DLRTVLRRSG CKNEKIAFIM DESNVLDSG FLERMNTLLA NGEVPGLFEG DEYATLMTQC KEGAQKEGLM LDSHEELYKW FTSQVIRNLH VVFTMNPSSE GLKDRAATSP ALFNRCVLN WFGDWSTEAL YQVGKEFTSK MDLEKPNYIV PDYMPVVYDK LPQPPSHREA IVNSCVFVHQ TLHQANARLA K RGGRTMAI TPRHYLDFIN HYANLFHEKR SELEEQQMHL NVGLRKIKET VDQVEELRRD LRIKSQELEV KNAAANDKLK KM VKDQQEA EKKKVMSQEI QEQLHKQQEV IADKQMSVKE DLDKVEPAVI EAQNAVKSIK KQHLVEVRSM ANPPAAVKLA LES ICLLLG ESTTDWKQIR SIIMRENFIP TIVNFSAEEI SDAIREKMKK NYMSNPSYNY EIVNRASLAC GPMVKWAIAQ LNYA DMLKR VEPLRNELQK LEDDAKDNQQ KANEVEQMIR DLEASIARYK EEYAVLISEA QAIKADLAAV EAKVNRSTAL LKSLS AERE RWEKTSETFK NQMSTIAGDC LLSAAFIAYA GYFDQQMRQN LFTTWSHHLQ QANIQFRTDI ARTEYLSNAD ERLRWQ ASS LPADDLCTEN AIMLKRFNRY PLIIDPSGQA TEFIMNEYKD RKITRTSFLD DAFRKNLESA LRFGNPLLVQ DVESYDP VL NPVLNREVRR TGGRVLITLG DQDIDLSPSF VIFLSTRDPT VEFPPDLCSR VTFVNFTVTR SSLQSQCLNE VLKAERPD V DEKRSDLLKL QGEFQLRLRQ LEKSLLQALN EVKGRILDDD TIITTLENLK REAAEVTRKV EETDIVMQEV ETVSQQYLP LSTACSSIYF TMESLKQIHF LYQYSLQFFL DIYHNVLYEN PNLKGVTDHT QRLSIITKDL FQVAFNRVAR GMLHQDHITF AMLLARIKL KGTVGEPTYD AEFQHFLRGN EIVLSAGSTP RIQGLTVEQA EAVVRLSCLP AFKDLIAKVQ ADEQFGIWLD S SSPEQTVP YLWSEETPAT PIGQAIHRLL LIQAFRPDRL LAMAHMFVST NLGESFMSIM EQPLDLTHIV GTEVKPNTPV LM CSVPGYD ASGHVEDLAA EQNTQITSIA IGSAEGFNQA DKAINTAVKS GRWVMLKNVH LAPGWLMQLE KKLHSLQPHA CFR LFLTME INPKVPVNLL RAGRIFVFEP PPGVKANMLR TFSSIPVSRI CKSPNERARL YFLLAWFHAI IQERLRYAPL GWSK KYEFG ESDLRSACDT VDTWLDDTAK GRQNISPDKI PWSALKTLMA QSIYGGRVDN EFDQRLLNTF LERLFTTRSF DSEFK LACK VDGHKDIQMP DGIRREEFVQ WVELLPDTQT PSWLGLPNNA ERVLLTTQGV DMISKMLKMQ MLEDEDDLAY AETEKK TRT DSTSDGRPAW MRTLHTTASN WLHLIPQTLS HLKRTVENIK DPLFRFFERE VKMGAKLLQD VRQDLADVVQ VCEGKKK QT NYLRTLINEL VKGILPRSWS HYTVPAGMTV IQWVSDFSER IKQLQNISLA AASGGAKELK NIHVCLGGLF VPEAYITA T RQYVAQANSW SLEELCLEVN VTTSQGATLD ACSFGVTGLK LQGATCNNNK LSLSNAISTA LPLTQLRWVK QTNTEKKAS VVTLPVYLNF TRADLIFTVD FEIATKEDPR SFYERGVAVL CTE

UniProtKB: Cytoplasmic dynein 1 heavy chain 1

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 3 / 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 #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.25 µm / Nominal defocus min: 0.61 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8dyu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13958
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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