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- EMDB-46843: Motor domain of dynein-1 complex on microtubules -

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Basic information

Entry
Database: EMDB / ID: EMD-46843
TitleMotor domain of dynein-1 complex on microtubules
Map dataMotor domain of dynein bound to microtubules in the presence of AMPPNP
Sample
  • Complex: Motor domain of dynein on microtubules
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordsdynein / microtubule / MOTOR PROTEIN
Function / homology
Function and homology information


dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / microtubule-based movement / dynein intermediate chain binding / microtubule / cell division / ATP 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
Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRao Q / Chai P / Zhang K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142959 United States
CitationJournal: bioRxiv / Year: 2024
Title: Molecular basis for the assembly of the dynein transport machinery on microtubules.
Authors: Qinhui Rao / Pengxin Chai / Kai Zhang /
Abstract: Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has ...Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has been elusive. Here, we reveal detailed structural insights into microtubule-mediated DDA assembly using cryo-electron microscopy. We find that an adaptor-independent dynein-dynactin complex (DD) predominantly forms on microtubules in an intrinsic 2:1 stoichiometry, induced by spontaneous parallelization of dynein upon microtubule binding. Adaptors can squeeze in and exchange within the assembled microtubule-bound DD complex, which is enabled by relative rotations between dynein and dynactin, and further facilitated by dynein light intermediate chains that assist in an adaptor 'search' mechanism. Our findings elucidate the dynamic adaptability of the dynein transport machinery, and reveal a new mode for assembly of the motile complex.
History
DepositionSep 3, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46843.png

Downloads & links

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Map

FileDownload / File: emd_46843.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMotor domain of dynein bound to microtubules in the presence of AMPPNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 333.312 Å		1.3 Å/pix.
x 256 pix.
= 333.312 Å		1.3 Å/pix.
x 256 pix.
= 333.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0932932 - 1.8131381
Average (Standard dev.)-0.0022769454 (±0.0459769)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 333.312 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half

Fileemd_46843_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_46843_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 of dynein on microtubules

EntireName: Motor domain of dynein on microtubules
Components
  • Complex: Motor domain of dynein on microtubules
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Motor domain of dynein on microtubules

SupramoleculeName: Motor domain of dynein on microtubules / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sus scrofa (pig)

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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: Sus scrofa (pig)
Molecular weightTheoretical: 532.739562 KDa
SequenceString: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRAPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES ...String:
MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRAPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES GKADRDGDKM APSVEKKIAE LEMGLLHLQQ NIEIPEISLP IHPIITNVAK QCYERGEKPK VTDFGDKVED PT FLNQLQS GVNRWIREIQ KVTKLDRDPA SGTALQEISF WLNLERALYR IQEKRESPEV LLTLDILKHG KRFHATVSFD TDT GLKQAL ETVNDYNPLM KDFPLNDLLS ATELDKIRQA LVAIFTHLRK IRNTKYPIQR ALRLVEAISR DLSSQLLKVL GTRK LMHVA YEEFEKVMVA CFEVFQTWDD EYEKLQVLLR DIVKRKREEN LKMVWRINPA HRKLQARLDQ MRKFRRQHEQ LRAVI VRVL RPQVTAVAQQ NQGEAPEPQD MKVAEVLFDA ADANAIEEVN LAYENVKEVD GLDVSKEGTE AWEAAMKRYD ERIDRV ETR ITARLRDQLG TAKNANEMFR IFSRFNALFV RPHIRGAIRE YQTQLIQRVK DDIESLHDKF KVQYPQSQAC KMSHVRD LP PVSGSIIWAK QIDRQLTAYM KRVEDVLGKG WENHVEGQKL KQDGDSFRMK LNTQEIFDDW ARKVQQRNLG VSGRIFAI E STRVRGRSGN VLKLKVNFLP EIITLSKEVR NLKWLGFRVP LAIVNKAHQA NQLYPFAISL IESVRTYERT CEKVEERNT ISLLVAGLKK EVQALIAEGI ALVWESYKLD PYVQRLAETV FNFQEKVDDL LIIEEKIDLE VRSLETCVYD HKTFSEILNR VQKAVDDLN LHSYSNLPIW VNKLDMEIER ILGVRLQAGL RAWTQVLLGQ AEDKAEVDMD TDAPQVSHKP GGEPKIKNVV H ELRITNQV IYLNPPIEEC RYKLYQEMFA WKMVVLSLPR IQSQRYQVGV HYELTEEEKF YRNALTRMPD GPVALEESYS AV MGIVTEV EQYVKVWLQY QCLWDMQAEN IYNRLGEDLN KWQALLVQIR KARGTFDNAE TKKEFGPVVI DYGKVQSKVN LKY DSWHKE VLSKFGQMLG SNMTEFHSQI SKSRQELEQH SVDTASTSDA VTFITYVQSL KRKIKQFEKQ VELYRNGQRL LEKQ RFQFP PSWLYIDNIE GEWGAFNDIM RRKDSAIQQQ VANLQMKIVQ EDRAVESRTT DLLADWEKTK PVTGNLRPEE ALQAL TIYE GKFGRLKDDR EKCAKAKEAL ELTETGLLSG SEERVQVALE ELQDLKGVWS ELSKIWEQID QMKEQPWVSV QPRKLR QNL DGLLNQLKNF PARLRQYASY EFVQRLLKGY LKINMLVIEL KSEALKDRHW KQLMKRLHVN WVVSELTLGQ IWDVDLQ KN EAVVKDVLLV AQGEMALEEF LKQIREVWNT YELDLVNYQN KCRLIRGWDD LFNKVKEHIN SVSAMKLSPY YKVFEEDA L SWEDKLNRIM ALFDVWIDVQ RRWVYLEGIF TGSADIKHLL PVETQRFQSI STEFLALMKK VSKSPLVMDV LNIQGVQRS LERLADLLGK IQKALGEYLE RERSSFPRFY FVGDEDLLEI IGNSKNVAKL QKHFKKMFAG VSSIILSEDN SVVLGISSRE GEEVTFKTP VSITEHPKIN EWLTLVEKEM RVTLAKLLAE SVTEVEIFGK ATSIDPNTYI TWIDKYQAQL VVLSAQIAWS E NVEAALSS IGGSGDSAPL QSVLSNVEVT LNVLADSVLM EQPPLRRRKL EHLITELVHQ RDVTRSLIKS KIDNAKSFEW LS QMRFYFD PKQTDVLQQL SIQMANAKFN YGFEYLGVQD KLVQTPLTDR CYLTMTQALE ARLGGSPFGP AGTGKTESVK ALG HQLGRF VLVFNCDETF DFQAMGRIFV GLCQVGAWGC FDEFNRLEER MLSAVSQQVQ CIQEALREHS SPNHDKASAP ITCE LLNKQ VKVSPDMAIF ITMNPGYAGR SNLPDNLKKL FRSLAMTKPD RQLIAQVMLY SQGFRTAEVL ANKIVPFFKL CDEQL SSQS HYDFGLRALK SVLVSAGNVK RERIQKIKRE KEERGEAVDE GEIAENLPEQ EILIQSVCET MVPKLVAEDI PLLFSL LSD VFPGVQYHRG EMTALREELK KVCQEMYLTY GDGEEVGGMW VEKVLQLYQI TQINHGLMMV GPSGSGKSMA WRVLLKA LE RLEGVEGVAH IIDPKAISKD HLYGTLDPNT REWTDGLFTH VLRKIIDNVR GELQKRQWIV FDGDVDPEWV ENLNSVLD D NKLLTLPNGE RLSLPPNVRI MFEVQDLKYA TLATVSRCGM VWFSEDVLST DMIFNNFLAR LRSIPLDEGE DEAQRRRKG KEDEGEEAAS PMLQIQRDAA TTLQPYFTPN GLVTKALEHA FKLEHIMDLT RLRCLGSLFS MLHQACRNVA QYNANHPDFP MQMEQLERY IQRYLVYAIL WSLSGDSRLK MRAELGEYIR RITTVPLPAA PNIPIIDYEV SISGEWSPWQ AKVPQIEVET H KVAAPDVV VPTLDTVRHE ALLYTWLAEH KPLVLCGPPG SGKTMTLFSA LRALPDMEVV GLNFSSATTP ELLLKTFDHY CE YRRTPNG VVLAPVQLGK WLVLFCDEIN LPDMDKYGTQ RVISFIRQMV EHGGFYRTSD QTWVKLERIQ FVGACNPPTD PGR KPLSHR FLRHVPVVYV DYPGPASLTQ IYGTFNRAML RLVPSLRTYA EPLTAAMVEF YTMSQERFTQ DTQPHYIYSP REMT RWVRG IFEALRPLET LPVEGLIRIW AHEALRLFQD RLVEDEERRW TDENIDLVAL KHFPNIDKEK AMSRPILYSN WLSKD YIPV DQEELRDYVK ARLKVFYEEE LDVPLVLFNE VLDHVLRIDR IFRQPQGHLL LIGVSGAGKT TLSRFVAWMN GLSVYQ IKV HRKYTGEDFD EDLRTVLRRS GCKNEKIAFI MDESNVLDSG FLERMNTLLA NGEVPGLFEG DEYATLMTQC KEGAQKE GL MLDSHEELYK WFTSQVIRNL HVVFTMNPSS EGLKDRAATS PALFNRCVLN WFGDWSTEAL YQVGKEFTSK MDLEKPNY V VPDYMPVVYD KLPQPPSHRE AIVNSCVFVH QTLHQANARL AKRGGRTMAI TPRHYLDFIN HYANLFHEKR SELEEQQMH LNVGLRKIKE TVDQVEELRR DLRIKSQELE VKNAAANDKL KKMVKDQQEA EKKKVMSQEI QEQLHKQQEV IADKQMSVKE DLDKVEPAV IEAQNAVKSI KKQHLVEVRS MANPPAAVKL ALESICLLLG ESTTDWKQIR SIIMRENFIP TIVNFSAEEI S DAIREKMK KNYMSNPSYN YEIVNRASLA CGPMVKWAIA QLNYADMLKR VEPLRNELQK LEDDAKDNQQ KANEVEQMIR DL EASIARY KEEYAVLISE AQAIKADLAA VEAKVNRSTA LLKSLSAERE RWEKTSETFK NQMSTIAGDC LLSAAFIAYA GYF DQQMRQ NLFTTWSHHL QQANIQFRTD IARTEYLSNA DERLRWQASS LPADDLCTEN AIMLKRFNRY PLIIDPSGQA TEFI MNEYK DRKITRTSFL DDAFRKNLES ALRFGNPLLV QDVESYDPVL NPVLNREVRR TGGRVLITLG DQDIDLSPSF VIFLS TRDP TVEFPPDLCS RVTFVNFTVT RSSLQSQCLN EVLKAERPDV DEKRSDLLKL QGEFQLRLRQ LEKSLLQALN EVKGRI LDD DTIITTLENL KREAAEVTRK VEETDIVMQE VETVSQQYLP LSTACSSIYF TMESLKQIHF LYQYSLQFFL DIYHNVL YE NPNLKGVTDH TQRLCIITKD LFQVAFNRVA RGMLHQDHIT FAMLLARIKL KGTVGEPTYE AEFQHFLRGK EIVLSAGS T PKIPGLTVEQ AEAVVRLSCL PAFKDLIAKV QADEQFSIWL DSSSPEQTVP HLWSEENPAT PIGQAIHRLL LIQAFRPDR LLAMAHVFVS TNLGESFMSI MEQPLDLTHI VDTEVKPNTP VLMCSVPGYD ASGHVEDLAA EQNTQITSIA IGSAEGFNQA DKAINTAVK SGRWVMLKNV HLAPGWLMQL EKKLHSLQPH ACFRLFLTME INPKVPVNLL RAGRIFVFEP PPGVKANMLR T FSSVPVSR ICKSPNERAR LYFLLAWFHA IIQERLRYAP LGWSKKYEFG ESDLRSACDT VDTWLDDTAK GRQNISPDKI PW SALKTLM AQSIYGGRVD NEFDQRLLNT FLERLFTTRS FDSEFKLACK VDGHKDIQMP DGIRREEFVQ WVELLPDTQT PSW LGLPNN AERVLLTTQG VDMISKMLKM QMLEDEDDLA YAETEKKTRT DSTADGRPAW MRTLHTTASN WLHLIPQTLS HLKR TVDNI KDPLFRFFER EVKMGARLLQ DVRQDLADVV QVCEGKKKQT NYLRTLINEL VKGILPRSWS HYTVPAGMTV IQWVS DFSE RIKQLQSVSQ AAASGGAKEL KNIHVCLGGL FVPEAYITAT RQYVAQANSW SLEELCLEVI VTTSQSATLD ACSFGV TGL KLQGATCSNN KLSLSNAIST VLPLTQLRWV KQTNAEKKAN VVTLPVYLNF TRADLIFTVD FEIATKEDPR SFYERGV AV LCTE

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: 1 / 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: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / 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: 7.2
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 opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106660
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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