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- EMDB-28999: Engineered human dynein motor domain in microtubule-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-28999
TitleEngineered human dynein motor domain in microtubule-bound state
Map dataSharpened map of human dynein motor domain in microtubule-bound mutant (dynein MT-B)
Sample
  • Complex: Engineered human dynein motor domain in microtubule-bound state
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDynein / motor domain / microtubule-bound / MOTOR PROTEIN
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / 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 ...selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / 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 / minus-end-directed microtubule motor activity / retrograde axonal transport / cytoplasmic dynein complex / dynein light intermediate chain binding / P-body assembly / nuclear migration / dynein intermediate chain binding / cytoplasmic microtubule / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic spindle organization / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / 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 / membrane / cytosol / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region ...Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / 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 / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 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 / Serine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTon W / Wang Y / Chai P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142959 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD023603 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport.
Authors: William D Ton / Yue Wang / Pengxin Chai / Cisloynny Beauchamp-Perez / Nicholas T Flint / Lindsay G Lammers / Hao Xiong / Kai Zhang / Steven M Markus /
Abstract: The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 ...The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 binding is required for dynein activity, its unbinding prior to initiation of cargo transport is equally important, since preventing dissociation leads to dynein dysfunction. To understand whether and how dynein-LIS1 binding is modulated, we engineered dynein mutants locked in a microtubule-bound (MT-B) or microtubule-unbound (MT-U) state. Whereas the MT-B mutant exhibits low LIS1 affinity, the MT-U mutant binds LIS1 with high affinity, and as a consequence remains almost irreversibly associated with microtubule plus-ends. We find that a monomeric motor domain is sufficient to exhibit these opposing LIS1 affinities, and that this is evolutionarily conserved between yeast and humans. Three cryo-EM structures of human dynein with and without LIS1 reveal microtubule-binding induced conformational changes responsible for this regulation. Our work reveals key biochemical and structural insight into LIS1-mediated dynein activation.
History
DepositionDec 1, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28999.png

Downloads & links

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Map

FileDownload / File: emd_28999.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of human dynein motor domain in microtubule-bound mutant (dynein MT-B)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 360 pix.
= 413.64 Å		1.15 Å/pix.
x 360 pix.
= 413.64 Å		1.15 Å/pix.
x 360 pix.
= 413.64 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.149 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.9771221 - 1.660737
Average (Standard dev.)0.0003507752 (±0.044137098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 413.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28999_msk_1.map
Projections & Slices
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Additional map: Unsharpened map of human dynein motor domain in...

Fileemd_28999_additional_1.map
AnnotationUnsharpened map of human dynein motor domain in microtubule-bound mutant (dynein MT-B)
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map A of human dynein motor domain...

Fileemd_28999_half_map_1.map
AnnotationHalf map A of human dynein motor domain with microtubule-bound mutant (dynein MT-B)
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of human dynein motor domain...

Fileemd_28999_half_map_2.map
AnnotationHalf map B of human dynein motor domain with microtubule-bound mutant (dynein MT-B)
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Engineered human dynein motor domain in microtubule-bound state

EntireName: Engineered human dynein motor domain in microtubule-bound state
Components
  • Complex: Engineered human dynein motor domain in microtubule-bound state
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Engineered human dynein motor domain in microtubule-bound state

SupramoleculeName: Engineered human dynein motor domain in microtubule-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase

MacromoleculeName: Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase
type: protein_or_peptide / ID: 1
Details: residues 1458-3281 of dynein followed by residues 30-96 of serine-tRNA ligase, followed by residues 3412-4646 of dynein
Number of copies: 1 / Enantiomer: LEVO / EC number: serine-tRNA ligase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 357.931625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSALEEFLKQ IREVWNTYEL DLVNYQNKCR LIRGWDDLFN KVKEHINSVS AMKLSPYYKV FEEDALSWED KLNRIMALFD VWIDVQRRW VYLEGIFTGS ADIKHLLPVE TQRFQSISTE FLALMKKVSK SPLVMDVLNI QGVQRSLERL ADLLGKIQKA L GEYLERER ...String:
GSALEEFLKQ IREVWNTYEL DLVNYQNKCR LIRGWDDLFN KVKEHINSVS AMKLSPYYKV FEEDALSWED KLNRIMALFD VWIDVQRRW VYLEGIFTGS ADIKHLLPVE TQRFQSISTE FLALMKKVSK SPLVMDVLNI QGVQRSLERL ADLLGKIQKA L GEYLERER SSFPRFYFVG DEDLLEIIGN SKNVAKLQKH FKKMFAGVSS IILNEDNSVV LGISSREGEE VMFKTPVSIT EH PKINEWL TLVEKEMRVT LAKLLAESVT EVEIFGKATS IDPNTYITWI DKYQAQLVVL SAQIAWSENV ETALSSMGGG GDA APLHSV LSNVEVTLNV LADSVLMEQP PLRRRKLEHL ITELVHQRDV TRSLIKSKID NAKSFEWLSQ MRFYFDPKQT DVLQ QLSIQ MANAKFNYGF EYLGVQDKLV QTPLTDRCYL TMTQALEARL GGSPFGPAGT GKTESVKALG HQLGRFVLVF NCDET FDFQ AMGRIFVGLC QVGAWGCFDE FNRLEERMLS AVSQQVQCIQ EALREHSNPN YDKTSAPITC ELLNKQVKVS PDMAIF ITM NPGYAGRSNL PDNLKKLFRS LAMTKPDRQL IAQVMLYSQG FRTAEVLANK IVPFFKLCDE QLSSQSHYDF GLRALKS VL VSAGNVKRER IQKIKREKEE RGEAVDEGEI AENLPEQEIL IQSVCETMVP KLVAEDIPLL FSLLSDVFPG VQYHRGEM T ALREELKKVC QEMYLTYGDG EEVGGMWVEK VLQLYQITQI NHGLMMVGPS GSGKSMAWRV LLKALERLEG VEGVAHIID PKAISKDHLY GTLDPNTREW TDGLFTHVLR KIIDSVRGEL QKRQWIVFDG DVDPEWVENL NSVLDDNKLL TLPNGERLSL PPNVRIMFE VQDLKYATLA TVSRCGMVWF SEDVLSTDMI FNNFLARLRS IPLDEGEDEA QRRRKGKEDE GEEAASPMLQ I QRDAATIM QPYFTSNGLV TKALEHAFQL EHIMDLTRLR CLGSLFSMLH QACRNVAQYN ANHPDFPMQI EQLERYIQRY LV YAILWSL SGDSRLKMRA ELGEYIRRIT TVPLPTAPNI PIIDYEVSIS GEWSPWQAKV PQIEVETHKV AAPDVVVPTL DTV RHEALL YTWLAEHKPL VLCGPPGSGK TMTLFSALRA LPDMEVVGLN FSSATTPELL LKTFDHYCEY RRTPNGVVLA PVQL GKWLV LFCDEINLPD MDKYGTQRVI SFIRQMVEHG GFYRTSDQTW VKLERIQFVG ACNPPTDPGR KPLSHRFLRH VPVVY VDYP GPASLTQIYG TFNRAMLRLI PSLRTYAEPL TAAMVEFYTM SQERFTQDTQ PHYIYSPREM TRWVRGIFEA LRPLET LPV EGLIRIWAHE ALRLFQDRLV EDEERRWTDE NIDTVALKHF PNIDREKAMS RPILYSNWLS KDYIPVDQEE LRDYVKA RL KVFYEEELDV PLVLFNEVLD HVLRIDRIFR QPQGHLLLIG VSGAGKTTLS RFVAWMNGLS VYQIKVHRKY TGEDFDED L RTVLRRSGCK NEKIAFIMDE SNVLDSGFLE RMNTLLANGE VPGLFEGDEY ATLMTQCKEG AQKEGLMLDS HEELYKWFT SQVIRNLHVV FTMNPSSEGL KDRAATSPAL FNRCVLNWFG DWSTEALYQV GKEFTSKMDL EKPNYIVPDY MPVVYDKLPQ PPSHREAIV NSCVFVHQTL HQANARLAKR GGRTMAITPR HYLDFINHYA NLFHEKRSEL EEQQMHLNVG LRKIKETVDQ V EELRRDLR IKSQELEVKN AAANDKLKKM VKDQQEAEKK KVMSQEIQEQ LHKQQEVIAD KQMSVKEDLL ALDQEVQELK KR LQEVQTE RNQVAKRVPK APPEEKEALI ARGRALGEEA KRLEEALREK EAQLEALRNE LQKLEDDAKD NQQKANEVEQ MIR DLEASI ARYKEEYAVL ISEAQAIKAD LAAVEAKVNR STALLKSLSA ERERWEKTSE TFKNQMSTIA GDCLLSAAFI AYAG YFDQQ MRQNLFTTWS HHLQQANIQF RTDIARTEYL SNADERLRWQ ASSLPADDLC TENAIMLKRF NRYPLIIDPS GQATE FIMN EYKDRKITRT SFLDDAFRKN LESALRFGNP LLVQDVESYD PVLNPVLNRE VRRTGGRVLI TLGDQDIDLS PSFVIF LST RDPTVEFPPD LCSRVTFVNF TVTRSSLQSQ CLNEVLKAER PDVDEKRSDL LKLQGEFQLR LRQLEKSLLQ ALNEVKG RI LDDDTIITTL ENLKREAAEV TRKVEETDIV MQEVETVSQQ YLPLSTACSS IYFTMESLKQ IHFLYQYSLQ FFLDIYHN V LYENPNLKGV TDHTQRLSII TKDLFQVAFN RVARGMLHQD HITFAMLLAR IKLKGTVGEP TYDAEFQHFL RGNEIVLSA GSTPRIQGLT VEQAEAVVRL SCLPAFKDLI AKVQADEQFG IWLDSSSPEQ TVPYLWSEET PATPIGQAIH RLLLIQAFRP DRLLAMAHM FVSTNLGESF MSIMEQPLDL THIVGTEVKP NTPVLMCSVP GYDASGHVED LAAEQNTQIT SIAIGSAEGF N QADKAINT AVKSGRWVML KNVHLAPGWL MQLEKKLHSL QPHACFRLFL TMEINPKVPV NLLRAGRIFV FEPPPGVKAN ML RTFSSIP VSRICKSPNE RARLYFLLAW FHAIIQERLR YAPLGWSKKY EFGESDLRSA CDTVDTWLDD TAKGRQNISP DKI PWSALK TLMAQSIYGG RVDNEFDQRL LNTFLERLFT TRSFDSEFKL ACKVDGHKDI QMPDGIRREE FVQWVELLPD TQTP SWLGL PNNAERVLLT TQGVDMISKM LKMQMLEDED DLAYAETEKK TRTDSTSDGR PAWMRTLHTT ASNWLHLIPQ TLSHL KRTV ENIKDPLFRF FEREVKMGAK LLQDVRQDLA DVVQVCEGKK KQTNYLRTLI NELVKGILPR SWSHYTVPAG MTVIQW VSD FSERIKQLQN ISLAAASGGA KELKNIHVCL GGLFVPEAYI TATRQYVAQA NSWSLEELCL EVNVTTSQGA TLDACSF GV TGLKLQGATC NNNKLSLSNA ISTALPLTQL RWVKQTNTEK KASVVTLPVY LNFTRADLIF TVDFEIATKE DPRSFYER G VAVLCTEEF

UniProtKB: Cytoplasmic dynein 1 heavy chain 1, Serine--tRNA ligase, 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
Details: 50 mM Tris pH 7.4, 150 mM potassium acetate, 2 mM magnesium acetate, 1 mM EGTA, 1 mM DTT, and 0.1 mM Mg-ATP
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 36000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE / Details: Ab-initio model was generated in cryoSPARC.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 44752
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8fcy:
Engineered human dynein motor domain in microtubule-bound state

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