EMDB-14552: The barbed end complex of dynactin bound to BICDR1 and the cytopl...

Basic information

Entry

Database: EMDB / ID: EMD-14552

• Title: The barbed end complex of dynactin bound to BICDR1 and the cytoplasmic dynein tails (A2, B1, B2)
• Map data: The barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2). 1.2445 A/pix.

Sample

• Complex: Complex of dynein, dynactin, and BICDR1 bound to microtubules
  • Organelle or cellular component: Dynein, cytoplasmic 1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2
  • Organelle or cellular component: Dynactin
    • Protein or peptide: ARP1 actin related protein 1 homolog A
    • Protein or peptide: Capping protein (Actin filament) muscle Z-line, alpha 1
    • Protein or peptide: F-actin capping protein beta subunit
  • Organelle or cellular component: BICDR1
    • Protein or peptide: BICD family-like cargo adapter 1
• Ligand: ADENOSINE-5'-DIPHOSPHATE
• Ligand: MAGNESIUM ION

Function / homology

Function:

Golgi to secretory granule transport / transport along microtubule / dynein light chain binding / WASH complex / F-actin capping protein complex / dynein heavy chain binding / negative regulation of filopodium assembly / positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / vesicle transport along microtubule / P-body assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / barbed-end actin filament capping / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / regulation of cell morphogenesis / regulation of lamellipodium assembly / nuclear migration / centrosome localization / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / dynactin binding / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / cytoplasmic microtubule organization / Mitotic Prometaphase / cytoskeleton organization / regulation of mitotic spindle organization / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / sarcomere / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cell morphogenesis / microtubule cytoskeleton organization / kinetochore / small GTPase binding / Aggrephagy / HCMV Early Events / neuron projection development / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / actin filament binding / late endosome / actin binding / positive regulation of cold-induced thermogenesis / cell cortex / actin cytoskeleton organization / vesicle / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / cytosol / cytoplasm

Domain/homology:

Dynein 1 light intermediate chain / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / 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 / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / 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, 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 / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats circular profile. / 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

Component:

BICD family-like cargo adapter 1 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Alpha-centractin / Cytoplasmic dynein 1 light intermediate chain 2 / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1

• Biological species: Homo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse) / pig (pig)
• Method: single particle reconstruction / cryo EM / Resolution: 3.3 Å
• Authors: Chaaban S / Carter AP

Funding support

United Kingdom, European Union, 3 items

Organization	Grant number	Country
Wellcome Trust	210711/Z/18/Z	United Kingdom
Medical Research Council (MRC, United Kingdom)	MC_UP_A025_1011	United Kingdom
European Molecular Biology Organization (EMBO)	ALTF 334-2020	European Union

• Citation: Journal: Nature / Year: 2022; Title: Structure of dynein-dynactin on microtubules shows tandem adaptor binding.; Authors: Sami Chaaban / Andrew P Carter / ; Abstract: Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour. Different coiled-coil adaptors are linked to different cargos, and some share motifs known to contact sites on dynein and dynactin. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.

History

Deposition	Mar 17, 2022	-
Header (metadata) release	Aug 17, 2022	-
Map release	Aug 17, 2022	-
Update	Oct 19, 2022	-
Current status	Oct 19, 2022	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_14552.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: The barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2). 1.2445 A/pix.
• Voxel size: X=Y=Z: 1.2445 Å

Density

Contour Level	By AUTHOR: 0.0244
Minimum - Maximum	-0.07608349 - 0.15971833
Average (Standard dev.)	1.7135379e-05 (±0.0009004926)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 768 768 768 Spacing 768 768 768
Cell	A=B=C: 955.776 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_14552_msk_1.map

Additional map: The barbed end complex of dynactin with BICDR-A...

• File: emd_14552_additional_1.map
• Annotation: The barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2). Unsharpenned map fit to the consensus map rescaled to 1.2445 A/pix.

Half map: Half map 1 of the barbed end complex...

• File: emd_14552_half_map_1.map
• Annotation: Half map 1 of the barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2) after fitting to the consensus map.

Half map: Half map 2 of the barbed end complex...

• File: emd_14552_half_map_2.map
• Annotation: Half map 2 of the barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2) after fitting to the consensus map.

Sample components

Entire : Complex of dynein, dynactin, and BICDR1 bound to microtubules

• Entire: Name: Complex of dynein, dynactin, and BICDR1 bound to microtubules

Components

• Complex: Complex of dynein, dynactin, and BICDR1 bound to microtubules
  • Organelle or cellular component: Dynein, cytoplasmic 1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2
  • Organelle or cellular component: Dynactin
    • Protein or peptide: ARP1 actin related protein 1 homolog A
    • Protein or peptide: Capping protein (Actin filament) muscle Z-line, alpha 1
    • Protein or peptide: F-actin capping protein beta subunit
  • Organelle or cellular component: BICDR1
    • Protein or peptide: BICD family-like cargo adapter 1
• Ligand: ADENOSINE-5'-DIPHOSPHATE
• Ligand: MAGNESIUM ION

Supramolecule #1: Complex of dynein, dynactin, and BICDR1 bound to microtubules

• Supramolecule: Name: Complex of dynein, dynactin, and BICDR1 bound to microtubules; type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
• Molecular weight: Theoretical: 130 KDa

Supramolecule #2: Dynein, cytoplasmic 1

• Supramolecule: Name: Dynein, cytoplasmic 1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #5-#7
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Supramolecule #3: Dynactin

• Supramolecule: Name: Dynactin / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1-#3
• Source (natural): Organism: Sus scrofa (pig)

Supramolecule #4: BICDR1

• Supramolecule: Name: BICDR1 / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #4
• Source (natural): Organism: Mus musculus (house mouse)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Macromolecule #1: ARP1 actin related protein 1 homolog A

• Macromolecule: Name: ARP1 actin related protein 1 homolog A / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
• Source (natural): Organism: pig (pig)
• Molecular weight: Theoretical: 42.670688 KDa

Sequence

String:

MESYDVIANQ PVVIDNGSGV IKAGFAGDQI PKYCFPNYVG RPKHVRVMAG ALEGDIFIGP KAEEHRGLLS IRYPMEHGIV KDWNDMERI WQYVYSKDQL QTFSEEHPVL LTEAPLNPRK NRERAAEVFF ETFNVPALFI SMQAVLSLYA TGRTTGVVLD S GDGVTHAV PIYEGFAMPH SIMRIDIAGR DVSRFLRLYL RKEGYDFHSS SEFEIVKAIK ERACYLSINP QKDETLETEK AQ YYLPDGS TIEIGPSRFR APELLFRPDL IGEESEGIHE VLVFAIQKSD MDLRRTLFSN IVLSGGSTLF KGFGDRLLSE VKK LAPKDV KIRISAPQER LYSTWIGGSI LASLDTFKKM WVSKKEYEED GARSIHRKTF

Macromolecule #2: Capping protein (Actin filament) muscle Z-line, alpha 1

• Macromolecule: Name: Capping protein (Actin filament) muscle Z-line, alpha 1; type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: pig (pig)
• Molecular weight: Theoretical: 33.059848 KDa

Sequence

String:

MADFEDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEVDGSLKS WRESCDSALR AYVKDHYSNG FCTVYAKNID GQQTIIACIE S HQFQPKNF WNGRWRSEWK FTITPPTAQV VGVLKIQVHY YEDGNVQLVS HKDVQDSVTV SNEAQTAKEF IKIIEHAENE YQ TAISENY QTMSDTTFKA LRRQLPVTRT KIDWNKILSY KIGKEMQNA

Macromolecule #3: F-actin capping protein beta subunit

• Macromolecule: Name: F-actin capping protein beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: pig (pig)
• Molecular weight: Theoretical: 30.669768 KDa

Sequence

String:

MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK LTSTVMLWLQ TNKSGSGTMN LGGSLTRQME KDETVSDCSP HIANIGRLVE DMENKIRSTL NEIYFGKTKD IV NGLRSVQ TFADKSKQEA LKNDLVEALK RKQQC

Macromolecule #4: BICD family-like cargo adapter 1

• Macromolecule: Name: BICD family-like cargo adapter 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 65.377035 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MSAFCLGLAG RASAPAEPDS ACCMELPAGA GDAVRSPATA AALVSFPGGP GELELALEEE LALLAAGERS SEPGEHPQAE PESPVEGHG PPLPPPPTQD PELLSVIRQK EKDLVLAARL GKALLERNQD MSRQYEQMHK ELTDKLEHLE QEKHELRRRF E NREGEWEG RVSELETDVK QLQDELERQQ LHLREADREK TRAVQELSEQ NQRLLDQLSR ASEVERQLSM QVHALKEDFR EK NSSTNQH IIRLESLQAE IKMLSDRKRE LEHRLSATLE ENDLLQGTVE ELQDRVLILE RQGHDKDLQL HQSQLELQEV RLS YRQLQG KVEELTEERS LQSSAATSTS LLSEIEQSME AEELEQEREQ LRLQLWEAYC QVRYLCSHLR GNDSADSAVS TDSS MDESS ETSSAKDVPA GSLRTALNDL KRLIQSIVDG VEPTVTLLSV EMTALKEERD RLRVTSEDKE PKEQLQKAIR DRDEA IAKK NAVELELAKC KMDMMSLNSQ LLDAIQQKLN LSQQLEAWQD DMHRVIDRQL MDTHLKEQSR PAAAAFPRGH GVGRGQ EPS TADGKRLFSF FRKI

Macromolecule #5: Cytoplasmic dynein 1 heavy chain 1

• Macromolecule: Name: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 533.08325 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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 PVETQRFQSI STEFLALMKK VSKSPLVMDV LNIQGVQRS LERLADLLGK 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

Macromolecule #6: Cytoplasmic dynein 1 intermediate chain 2

• Macromolecule: Name: Cytoplasmic dynein 1 intermediate chain 2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 71.546445 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVFSEY WVPPPMSPS SKSVSTPSEA GSQDSGDGAV GSRTLHWDTD PSVLQLHSDS DLGRGPIKLG MAKITQVDFP PREIVTYTKE T QTPVMAQP KEDEEEDDDV VAPKPPIEPE EEKTLKKDEE NDSKAPPHEL TEEEKQQILH SEEFLSFFDH STRIVERALS EQ INIFFDY SGRDLEDKEG EIQAGAKLSL NRQFFDERWS KHRVVSCLDW SSQYPELLVA SYNNNEDAPH EPDGVALVWN MKY KKTTPE YVFHCQSAVM SATFAKFHPN LVVGGTYSGQ IVLWDNRSNK RTPVQRTPLS AAAHTHPVYC VNVVGTQNAH NLIS ISTDG KICSWSLDML SHPQDSMELV HKQSKAVAVT SMSFPVGDVN NFVVGSEEGS VYTACRHGSK AGISEMFEGH QGPIT GIHC HAAVGAVDFS HLFVTSSFDW TVKLWTTKNN KPLYSFEDNA DYVYDVMWSP THPALFACVD GMGRLDLWNL NNDTEV PTA SISVEGNPAL NRVRWTHSGR EIAVGDSEGQ IVIYDVGEQI AVPRNDEWAR FGRTLAEINA NRADAEEEAA TRIPA

Macromolecule #7: Cytoplasmic dynein 1 light intermediate chain 2

• Macromolecule: Name: Cytoplasmic dynein 1 light intermediate chain 2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 54.173156 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MAPVGVEKKL LLGPNGPAVA AAGDLTSEEE EGQSLWSSIL SEVSTRARSK LPSGKNILVF GEDGSGKTTL MTKLQGAEHG KKGRGLEYL YLSVHDEDRD DHTRCNVWIL DGDLYHKGLL KFAVSAESLP ETLVIFVADM SRPWTVMESL QKWASVLREH I DKMKIPPE KMRELERKFV KDFQDYMEPE EGCQGSPQRR GPLTSGSDEE NVALPLGDNV LTHNLGIPVL VVCTKCDAVS VL EKEHDYR DEHLDFIQSH LRRFCLQYGA ALIYTSVKEE KNLDLLYKYI VHKTYGFHFT TPALVVEKDA VFIPAGWDNE KKI AILHEN FTTVKPEDAY EDFIVKPPVR KLVHDKELAA EDEQVFLMKQ QSLLAKQPAT PTRASESPAR GPSGSPRTQG RGGP ASVPS SSPGTSVKKP DPNIKNNAAS EGVLASFFNS LLSKKTGSPG SPGAGGVQST AKKSGQKTVL SNVQEELDRM TRKPD SMVT NSSTENEA

Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 6 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

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

Macromolecule #9: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 6 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

Buffer

pH: 7.2
Component:

Concentration	Formula	Name
30.0 mM	HEPES	4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
60.0 mM	KCl	Potassium chloride
5.0 mM	MgSO4	Magnesium sulfate
1.0 mM	EGTA	3,12-Bis(carboxymethyl)-6,9-dioxa-3,12-diazatetradecane-1,14-dioic acid
1.0 mM	DTT	Dithiothreitol
3.0 mM	AMPPNP	Adenylyl-imidodiphosphate
5.0 uM	TaxolPaclitaxel	Paclitaxel
0.01 %	IGEPAL	Octylphenoxypolyethoxyethanol

• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: 20 second incubation.

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
• Specialist optics: Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 14 / Number real images: 88715 / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Ų; Details: Images were collected in movie-mode and fractionated into 53 movie frames
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 179660

Atomic model buiding 1

• Refinement: Space: REAL / Protocol: FLEXIBLE FIT

Output model

PDB-7z8i:
The barbed end complex of dynactin bound to BICDR1 and the cytoplasmic dynein tails (A2, B1, B2)