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- EMDB-17829: Cytoplasmic dynein-1 A1/A2 motor domains bound to LIS1 -

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Basic information

Entry
Database: EMDB / ID: EMD-17829
TitleCytoplasmic dynein-1 A1/A2 motor domains bound to LIS1
Map data
Sample
  • Complex: Cytoplasmic dynein-A1/A2 motor domains bound to LIS1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
    • Protein or peptide: Dynactin subunit 1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDynein / AAA-Atpase / LIS1 / MOTOR PROTEIN
Function / homology
Function and homology information


corpus callosum morphogenesis / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / centriolar subdistal appendage / positive regulation of neuromuscular junction development / maintenance of centrosome location / centriole-centriole cohesion / platelet activating factor metabolic process ...corpus callosum morphogenesis / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / centriolar subdistal appendage / positive regulation of neuromuscular junction development / maintenance of centrosome location / centriole-centriole cohesion / platelet activating factor metabolic process / transport along microtubule / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / radial glia-guided pyramidal neuron migration / acrosome assembly / microtubule anchoring at centrosome / central region of growth cone / Recruitment of mitotic centrosome proteins and complexes / cerebral cortex neuron differentiation / dynein light chain binding / establishment of centrosome localization / microtubule sliding / ventral spinal cord development / dynein heavy chain binding / positive regulation of cytokine-mediated signaling pathway / positive regulation of embryonic development / microtubule organizing center organization / interneuron migration / layer formation in cerebral cortex / retromer complex / astral microtubule / microtubule plus-end / auditory receptor cell development / nuclear membrane disassembly / positive regulation of intracellular transport / cortical microtubule organization / positive regulation of microtubule nucleation / positive regulation of dendritic spine morphogenesis / reelin-mediated signaling pathway / myeloid leukocyte migration / regulation of metaphase plate congression / positive regulation of spindle assembly / melanosome transport / establishment of spindle localization / stereocilium / osteoclast development / microtubule plus-end binding / non-motile cilium assembly / brain morphogenesis / vesicle transport along microtubule / dynein complex / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / kinesin complex / P-body assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule motor activity / MHC class II antigen presentation / negative regulation of JNK cascade / Recruitment of NuMA to mitotic centrosomes / minus-end-directed microtubule motor activity / microtubule associated complex / cytoplasmic dynein complex / dynein light intermediate chain binding / COPI-mediated anterograde transport / motile cilium / stem cell division / neuromuscular process controlling balance / neuromuscular process / microtubule-based movement / nuclear migration / neuromuscular junction development / cell leading edge / motor behavior / dynein intermediate chain binding / dynein complex binding / germ cell development / transmission of nerve impulse / establishment of mitotic spindle orientation / dynactin binding / protein secretion / cochlea development / neuroblast proliferation / positive regulation of axon extension / microtubule-based process / lipid catabolic process / phospholipase binding / intercellular bridge / COPI-mediated anterograde transport / cytoplasmic microtubule / JNK cascade / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / neuron projection maintenance / axon cytoplasm / Mitotic Prometaphase
Similarity search - Function
: / : / PAC1 LisH domain / Dynein associated protein / Dynein associated protein / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 / LIS1, N-terminal / CAP-Gly domain signature. ...: / : / PAC1 LisH domain / Dynein associated protein / Dynein associated protein / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 / LIS1, N-terminal / CAP-Gly domain signature. / : / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / 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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynactin subunit 1 / Platelet-activating factor acetylhydrolase IB subunit beta / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsSingh K / Lau CK / Manigrasso G / Gassmann R / Carter AP
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust210711/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 197-2021European Union
CitationJournal: Science / Year: 2024
Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Authors: Kashish Singh / Clinton K Lau / Giulia Manigrasso / José B Gama / Reto Gassmann / Andrew P Carter /
Abstract: Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil ...Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.
History
DepositionJul 12, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17829.png

Downloads & links

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Map

FileDownload / File: emd_17829.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.24 Å		1.06 Å/pix.
x 360 pix.
= 381.24 Å		1.06 Å/pix.
x 360 pix.
= 381.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
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Contour LevelBy AUTHOR: 0.0086
Minimum - Maximum-0.009898043 - 0.040373217
Average (Standard dev.)0.00034176942 (±0.0019117253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17829_msk_1.map
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Additional map: unsharpened map

Fileemd_17829_additional_1.map
Annotationunsharpened map
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Half map: #2

Fileemd_17829_half_map_1.map
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Half map: #1

Fileemd_17829_half_map_2.map
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Sample components

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Entire : Cytoplasmic dynein-A1/A2 motor domains bound to LIS1

EntireName: Cytoplasmic dynein-A1/A2 motor domains bound to LIS1
Components
  • Complex: Cytoplasmic dynein-A1/A2 motor domains bound to LIS1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
    • Protein or peptide: Dynactin subunit 1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cytoplasmic dynein-A1/A2 motor domains bound to LIS1

SupramoleculeName: Cytoplasmic dynein-A1/A2 motor domains bound to LIS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 533.055125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES ...String:
MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES GKADRDGDKM APSVEKKIAE LEMGLLHLQQ NIEIPEISLP IHPMITNVAK 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 NQGEVPEPQD MKVAEVLFDA ADANAIEEVN LAYENVKEVD GLDVSKEGTE AWEAAMKRYD ERIDRV ETR ITARLRDQLG TAKNANEMFR IFSRFNALFV RPHIRGAIRE YQTQLIQRVK DDIESLHDKF KVQYPQSQAC KMSHVRD LP PVSGSIIWAK QIDRQLTAYM KRVEDVLGKG WENHVEGQKL KQDGDSFRMK LNTQEIFDDW ARKVQQRNLG VSGRIFTI E STRVRGRTGN VLKLKVNFLP EIITLSKEVR NLKWLGFRVP LAIVNKAHQA NQLYPFAISL IESVRTYERT CEKVEERNT ISLLVAGLKK EVQALIAEGI ALVWESYKLD PYVQRLAETV FNFQEKVDDL LIIEEKIDLE VRSLETCMYD HKTFSEILNR VQKAVDDLN LHSYSNLPIW VNKLDMEIER ILGVRLQAGL RAWTQVLLGQ AEDKAEVDMD TDAPQVSHKP GGEPKIKNVV H ELRITNQV IYLNPPIEEC RYKLYQEMFA WKMVVLSLPR IQSQRYQVGV HYELTEEEKF YRNALTRMPD GPVALEESYS AV MGIVSEV EQYVKVWLQY QCLWDMQAEN IYNRLGEDLN KWQALLVQIR KARGTFDNAE TKKEFGPVVI DYGKVQSKVN LKY DSWHKE VLSKFGQMLG SNMTEFHSQI SKSRQELEQH SVDTASTSDA VTFITYVQSL KRKIKQFEKQ VELYRNGQRL LEKQ RFQFP PSWLYIDNIE GEWGAFNDIM RRKDSAIQQQ VANLQMKIVQ EDRAVESRTT DLLTDWEKTK PVTGNLRPEE ALQAL TIYE GKFGRLKDDR EKCAKAKEAL ELTDTGLLSG SEERVQVALE ELQDLKGVWS ELSKVWEQID QMKEQPWVSV QPRKLR QNL DALLNQLKSF PARLRQYASY EFVQRLLKGY MKINMLVIEL KSEALKDRHW KQLMKRLHVN WVVSELTLGQ IWDVDLQ KN EAIVKDVLLV AQGEMALEEF LKQIREVWNT YELDLVNYQN KCRLIRGWDD LFNKVKEHIN SVSAMKLSPY YKVFEEDA L SWEDKLNRIM ALFDVWIDVQ RRWVYLEGIF TGSADIKHLL PVETQEFQSI STEFLALMKK VSKSPLVMDV LNIQGVQRS LERLADLLGE IQKALGEYLE RERSSFPRFY FVGDEDLLEI IGNSKNVAKL QKHFKKMFAG VSSIILNEDN SVVLGISSRE GEEVMFKTP VSITEHPKIN EWLTLVEKEM RVTLAKLLAE SVTEVEIFGK ATSIDPNTYI TWIDKYQAQL VVLSAQIAWS E NVETALSS MGGGGDAAPL HSVLSNVEVT LNVLADSVLM EQPPLRRRKL EHLITELVHQ RDVTRSLIKS KIDNAKSFEW LS QMRFYFD PKQTDVLQQL SIQMANAKFN YGFEYLGVQD KLVQTPLTDR CYLTMTQALE ARLGGSPFGP AGTGKTESVK ALG HQLGRF VLVFNCDETF DFQAMGRIFV GLCQVGAWGC FDEFNRLEER MLSAVSQQVQ CIQEALREHS NPNYDKTSAP 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 VLRKIIDSVR GELQKRQWIV FDGDVDPEWV ENLNSVLD D NKLLTLPNGE RLSLPPNVRI MFEVQDLKYA TLATVSRCGM VWFSEDVLST DMIFNNFLAR LRSIPLDEGE DEAQRRRKG KEDEGEEAAS PMLQIQRDAA TIMQPYFTSN GLVTKALEHA FQLEHIMDLT RLRCLGSLFS MLHQACRNVA QYNANHPDFP MQIEQLERY IQRYLVYAIL WSLSGDSRLK MRAELGEYIR RITTVPLPTA 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 RLIPSLRTYA EPLTAAMVEF YTMSQERFTQ DTQPHYIYSP REMT RWVRG IFEALRPLET LPVEGLIRIW AHEALRLFQD RLVEDEERRW TDENIDTVAL KHFPNIDREK 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 I 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 TQRLSIITKD LFQVAFNRVA RGMLHQDHIT FAMLLARIKL KGTVGEPTYD AEFQHFLRGN EIVLSAGS T PRIQGLTVEQ AEAVVRLSCL PAFKDLIAKV QADEQFGIWL DSSSPEQTVP YLWSEETPAT PIGQAIHRLL LIQAFRPDR LLAMAHMFVS TNLGESFMSI MEQPLDLTHI VGTEVKPNTP VLMCSVPGYD ASGHVEDLAA EQNTQITSIA IGSAEGFNQA DKAINTAVK SGRWVMLKNV HLAPGWLMQL EKKLHSLQPH ACFRLFLTME INPKVPVNLL RAGRIFVFEP PPGVKANMLR T FSSIPVSR ICKSPNERAR LYFLLAWFHA IIQERLRYAP LGWSKKYEFG ESDLRSACDT VDTWLDDTAK GRQNISPDKI PW SALKTLM AQSIYGGRVD NEFDQRLLNT FLERLFTTRS FDSEFKLACK VDGHKDIQMP DGIRREEFVQ WVELLPDTQT PSW LGLPNN AERVLLTTQG VDMISKMLKM QMLEDEDDLA YAETEKKTRT DSTSDGRPAW MRTLHTTASN WLHLIPQTLS HLKR TVENI KDPLFRFFER EVKMGAKLLQ DVRQDLADVV QVCEGKKKQT NYLRTLINEL VKGILPRSWS HYTVPAGMTV IQWVS DFSE RIKQLQNISL AAASGGAKEL KNIHVCLGGL FVPEAYITAT RQYVAQANSW SLEELCLEVN VTTSQGATLD ACSFGV TGL KLQGATCNNN KLSLSNAIST ALPLTQLRWV KQTNTEKKAS VVTLPVYLNF TRADLIFTVD FEIATKEDPR SFYERGV AV LCTE

UniProtKB: Cytoplasmic dynein 1 heavy chain 1

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Macromolecule #2: Platelet-activating factor acetylhydrolase IB subunit beta

MacromoleculeName: Platelet-activating factor acetylhydrolase IB subunit beta
type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.709984 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVLSQRQRDE LNRAIADYLR SNGYEEAYSV FKKEAELDVN EELDKKYAGL LEKKWTSVIR LQKKVMELES KLNEAKEEFT SGGPLGQKR DPKEWIPRPP EKYALSGHRS PVTRVIFHPV FSVMVSASED ATIKVWDYET GDFERTLKGH TDSVQDISFD H SGKLLASC ...String:
MVLSQRQRDE LNRAIADYLR SNGYEEAYSV FKKEAELDVN EELDKKYAGL LEKKWTSVIR LQKKVMELES KLNEAKEEFT SGGPLGQKR DPKEWIPRPP EKYALSGHRS PVTRVIFHPV FSVMVSASED ATIKVWDYET GDFERTLKGH TDSVQDISFD H SGKLLASC SADMTIKLWD FQGFECIRTM HGHDHNVSSV AIMPNGDHIV SASRDKTIKM WEVQTGYCVK TFTGHREWVR MV RPNQDGT LIASCSNDQT VRVWVVATKE CKAELREHEH VVECISWAPE SSYSSISEAT GSETKKSGKP GPFLLSGSRD KTI KMWDVS TGMCLMTLVG HDNWVRGVLF HSGGKFILSC ADDKTLRVWD YKNKRCMKTL NAHEHFVTSL DFHKTAPYVV TGSV DQTVK VWECR

UniProtKB: Platelet-activating factor acetylhydrolase IB subunit beta

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Macromolecule #3: Dynactin subunit 1

MacromoleculeName: Dynactin subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 142.015484 KDa
SequenceString: MAQSKRHVYS RTPSGSRMSA EASARPLRVG SRVEVIGKGH RGTVAYVGAT LFATGKWVGV ILDEAKGKND GTVQGRKYFT CDEGHGIFV RQSQIQVFED GADTTSPETP DSSASKVLRR EGTDSNAKTS KLRGPKPKKA PTARKTTTRR PKPTRPASTG V AGASSSLG ...String:
MAQSKRHVYS RTPSGSRMSA EASARPLRVG SRVEVIGKGH RGTVAYVGAT LFATGKWVGV ILDEAKGKND GTVQGRKYFT CDEGHGIFV RQSQIQVFED GADTTSPETP DSSASKVLRR EGTDSNAKTS KLRGPKPKKA PTARKTTTRR PKPTRPASTG V AGASSSLG PSGSASAGEL SSSEPSTPAQ TPLAAPIIPT PALTSPGAAP PLPSPSKEEE GLRAQVRDLE EKLETLRLKR AE DKAKLKE LEKHKIQLEQ VQEWKSKMQE QQADLQRRLK EARKEAKEAL EAKERYMEEM ADTADAIEMA TLDKEMAEER AES LQQEVE ALKERVDELT TDLEILKAEI EEKGSDGAAS SYQLKQLEEQ NARLKDALVR MRDLSSSEKQ EHVKLQKLME KKNQ ELEVV RQQRERLQEE LSQAESTIDE LKEQVDAALG AEEMVEMLTD RNLNLEEKVR ELRETVGDLE AMNEMNDELQ ENARE TELE LREQLDMAGA RVREAQKRVE AAQETVADYQ QTIKKYRQLT AHLQDVNREL TNQQEASVER QQQPPPETFD FKIKFA ETK AHAKAIEMEL RQMEVAQANR HMSLLTAFMP DSFLRPGGDH DCVLVLLLMP RLICKAELIR KQAQEKFDLS ENCSERP GL RGAAGEQLSF AAGLVYSLSL LQATLHRYEH ALSQCSVDVY KKVGSLYPEM SAHERSLDFL IELLHKDQLD ETVNVEPL T KAIKYYQHLY SIHLAEQPED STMQLADHIK FTQSALDCMS VEVGRLRAFL QGGQEASDIA LLLRDLETSC SDIRQFCKK IRRRMPGTDA PGIPAALAFG AQVSDTLLDC RKHLTWVVAV LQEVAAAAAQ LIAPLAENEG LPVAALEELA FKASEQIYGT PSSSPYECL RQSCNILIST MNKLATAMQE GEYDAERPPS KPPPVELRAA ALRAEITDAE GLGLKLEDRE TVIKELKKSL K IKGEELSE ANVRLSLLEK KLDSAAKDAD ERIEKVQTRL EETQALLRKK EKEFEETMDA LQADIDQLEA EKAELKQRLN SQ SKRTIEG IRGPPPSGIA TLVSGIAGEE QQRGGAPGQA PGIVPGPGLV KDSPLLLQQI SAMRLHISQL QHENSVLKGA QMK ASLAAL PPLHVAKLSL PPHEGPGSEL AAGALYRKTN QLLETLNQLS THTHVVDITR SSPAAKSPSA QLLEQVTQLK SLSD TIEKL KDEVLKETVS QRPGATVPTD FATFPSSAFL RAKEEQQDDT VYMGKVTFSC AAGLGQRHRL VLTQEQLHQL HDRLI S

UniProtKB: Dynactin subunit 1

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Macromolecule #4: Cytoplasmic dynein 1 intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 intermediate chain 2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.442141 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVPPPM SPSSKSVST PSEAGSQDSG DGAVGSRRGP IKLGMAKITQ VDFPPREIVT YTKETQTPVM AQPKEDEEED DDVVAPKPPI E PEEEKTLK ...String:
MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVPPPM SPSSKSVST PSEAGSQDSG DGAVGSRRGP IKLGMAKITQ VDFPPREIVT YTKETQTPVM AQPKEDEEED DDVVAPKPPI E PEEEKTLK KDEENDSKAP PHELTEEEKQ QILHSEEFLS FFDHSTRIVE RALSEQINIF FDYSGRDLED KEGEIQAGAK LS LNRQFFD ERWSKHRVVS CLDWSSQYPE LLVASYNNNE DAPHEPDGVA LVWNMKYKKT TPEYVFHCQS AVMSATFAKF HPN LVVGGT YSGQIVLWDN RSNKRTPVQR TPLSAAAHTH PVYCVNVVGT QNAHNLISIS TDGKICSWSL DMLSHPQDSM ELVH KQSKA VAVTSMSFPV GDVNNFVVGS EEGSVYTACR HGSKAGISEM FEGHQGPITG IHCHAAVGAV DFSHLFVTSS FDWTV KLWS TKNNKPLYSF EDNAGYVYDV MWSPTHPALF ACVDGMGRLD LWNLNNDTEV PTASISVEGN PALNRVRWTH SGREIA VGD SEGQIVIYDV GEQIAVPRND EWARFGRTLA EINANRADAE EEAATRIPA

UniProtKB: Cytoplasmic dynein 1 intermediate chain 2

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 31898
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7z8g


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8pqz:
Cytoplasmic dynein-1 A1/A2 motor domains bound to LIS1

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