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- EMDB-46953: CryoEM structures of yeast cytoplasmic dynein in the presence of ... -

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Entry
Database: EMDB / ID: EMD-46953
TitleCryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1.
Map data
Sample
  • Complex: yeast dynein in the presence of ATP and PAC1
    • Protein or peptide: Dynein heavy chain, cytoplasmic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsEnzyme / AAA protein / MOTOR PROTEIN
Function / homology
Function and homology information


karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration ...karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / DYN1, AAA+ ATPase lid 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 ...: / DYN1, AAA+ ATPase lid 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
Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKendrick AA / Leschziner AE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Multiple steps of dynein activation by Lis1 visualized by cryo-EM.
Authors: Agnieszka A Kendrick / Kendrick H V Nguyen / Wen Ma / Eva P Karasmanis / Rommie E Amaro / Samara L Reck-Peterson / Andres E Leschziner /
Abstract: Cytoplasmic dynein-1 (dynein) is an essential molecular motor controlled in part by autoinhibition. Lis1, a key dynein regulator mutated in the neurodevelopmental disease lissencephaly, plays a role ...Cytoplasmic dynein-1 (dynein) is an essential molecular motor controlled in part by autoinhibition. Lis1, a key dynein regulator mutated in the neurodevelopmental disease lissencephaly, plays a role in dynein activation. We recently identified a structure of partially autoinhibited dynein bound to Lis1, which suggests an intermediate state in dynein's activation pathway. However, other structural information is needed to fully understand how Lis1 activates dynein. Here, we used cryo-EM and yeast dynein and Lis1 incubated with ATP at different time points to reveal conformations that we propose represent additional intermediate states in dynein's activation pathway. We solved 16 high-resolution structures, including 7 distinct dynein and dynein-Lis1 structures from the same sample. Our data support a model in which Lis1 relieves dynein autoinhibition by increasing its basal ATP hydrolysis rate and promoting conformations compatible with complex assembly and motility. Together, this analysis advances our understanding of dynein activation and the contribution of Lis1 to this process.
History
DepositionSep 8, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46953.png

Downloads & links

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Map

FileDownload / File: emd_46953.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.)
0.89 Å/pix.
x 352 pix.
= 312.928 Å		0.89 Å/pix.
x 352 pix.
= 312.928 Å		0.89 Å/pix.
x 352 pix.
= 312.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.9112082 - 1.5175786
Average (Standard dev.)0.00074307586 (±0.026985183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 312.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46953_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_46953_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast dynein in the presence of ATP and PAC1

EntireName: yeast dynein in the presence of ATP and PAC1
Components
  • Complex: yeast dynein in the presence of ATP and PAC1
    • Protein or peptide: Dynein heavy chain, cytoplasmic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: yeast dynein in the presence of ATP and PAC1

SupramoleculeName: yeast dynein in the presence of ATP and PAC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c

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Macromolecule #1: Dynein heavy chain, cytoplasmic

MacromoleculeName: Dynein heavy chain, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 331.525 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GDQLTHVVEE VKTYDLVWRS IKNLWEDVQR TFETPWCRVD VLLLQSDLAN FLRRADELPR AVKQFEMYKS LFSQVNMLTS VNKILVELK DGALKPRHWN MIFRDIGKRQ IQKNLLDKLE FSLKDVMVLN LTLNEILLTK IIERAQKEFV IEKSLNRIKK F WKEAQYEV ...String:
GDQLTHVVEE VKTYDLVWRS IKNLWEDVQR TFETPWCRVD VLLLQSDLAN FLRRADELPR AVKQFEMYKS LFSQVNMLTS VNKILVELK DGALKPRHWN MIFRDIGKRQ IQKNLLDKLE FSLKDVMVLN LTLNEILLTK IIERAQKEFV IEKSLNRIKK F WKEAQYEV IEHSSGLKLV REWDVLEQAC KEDLEELVSM KASNYYKIFE QDCLDLESKL TKLSEIQVNW VEVQFYWLDL YG ILGENLD IQNFLPLETS KFKSLTSEYK MITTRAFQLD TTIEVIHIPN FDTTLKLTID SLKMIKSSLS TFLERQRRQF PRF YFLGND DLLKIIGSGK HHDQVSKFMK KMFGSIESII FFEDSITGVR SVEGEVLNLN EKIELKDSIQ AQEWLNILDT EIKL SVFTQ FRDCLGQLKD GTDIEVVVSK YIFQAILLSA QVMWTELVEK CLQTNEFSKY WKEVDMKIKG LLDKLNKSSD NVKKK IEAL LVEYLHFNNV IGQLKNCSTK EEARLLWAKV QKFYQKNDTL DDLNSVFISQ SGYLLQYKFE YIGIPERLIY TPLLLV GFA TLTDSLHQKY GGCFFGPAGT GKTETVKAFG QNLGRVVVVF NCDDSFDYQV LSRLLVGITQ IGAWGCFDEF NRLDEKV LS AVSANIQQIQ NGLQVGKSHI TLLEEETPLS PHTAVFITLN PGYNGRSELP ENLKKSFREF SMKSPQSGTI AEMILQIM G FEDSKSLASK IVHFLELLSS KCSSMNHYHF GLRTLKGVLR NCSPLVSEFG EGEKTVVESL KRVILPSLGD TDELVFKDE LSKIFDSAGT PLNSKAIVQC LKDAGQRSGF SMSEEFLKKC MQFYYMQKTQ QALILVGKAG CGKTATWKTV IDAMAIFDGH ANVVYVIDT KVLTKESLYG SMLKATLEWR DGLFTSILRR VNDDITGTFK NSRIWVVFDS DLDPEYVEAM NSVLDDNKIL T LPNGERLP IPPNFRILFE TDNLDHTTPA TITRCGLLWF STDVCSISSK IDHLLNKSYE ALDNKLSMFE LDKLKDLISD SF DMASLTN IFTCSNDLVH ILGVRTFNKL ETAVQLAVHL ISSYRQWFQN LDDKSLKDVI TLLIKRSLLY ALAGDSTGES QRA FIQTIN TYFGHDSQEL SDYSTIVIAN DKLSFSSFCS EIPSVSLEAH EVMRPDIVIP TIDTIKHEKI FYDLLNSKRG IILC GPPGS GKTMIMNNAL RNSSLYDVVG INFSKDTTTE HILSALHRHT NYVTTSKGLT LLPKSDIKNL VLFCDEINLP KLDKY GSQN VVLFLRQLME KQGFWKTPEN KWVTIERIHI VGACNPPTDP GRIPMSERFT RHAAILYLGY PSGKSLSQIY EIYYKA IFK LVPEFRSYTE PFARASVHLY NECKARYSTG LQSHYLFSPR ELTRLVRGVY TAINTGPRQT LRSLIRLWAY EAWRIFA DR LVGVKEKNSF EQLLYETVDK YLPNQDLGNI SSTSLLFSGL LSLDFKEVNK TDLVNFIEER FKTFCDEELE VPMVIHES M VDHILRIDRA LKQVQGHMML IGASRTGKTI LTRFVAWLNG LKIVQPKIHR HSNLSDFDMI LKKAISDCSL KESRTCLII DESNILETAF LERMNTLLAN ADIPDLFQGE EYDKLLNNLR NKTRSLGLLL DTEQELYDWF VGEIAKNLHV VFTICDPTNN KSSAMISSP ALFNRCIINW MGDWDTKTMS QVANNMVDVV PMEFTDFIVP EVNKELVFTE PIQTIRDAVV NILIHFDRNF Y QKMKVGVN PRSPGYFIDG LRALVKLVTA KYQDLQENQR FVNVGLEKLN ESVLKVNELN KTLSKKSTEL TEKEKEARST LD KMLMEQN ESERKQEATE EIKKILKVQE EDIRKRKEVV MKSIQDIEPT ILEAQRGVKN IKKQQLTEIR SMVNPPSGVK IVM EAVCAI LGYQFSNWRD IQQFIRKDDF IHNIVHYDTT LHMKPQIRKY MEEEFLSDPN FTYETINRAS KACGPLYQWV NAQI NFSKV LENVDPLRQE MKRIEFESLK TKANLLAAEE MTQDLEASIE VSKQKYSLLI RDVEAIKTEM SNVQANLDRS ISLVK SLTF EKERWLNTTK QFSKTSQELI GNCIISSIYE TYFGHLNERE RGDMLVILKR LLGKFAVKYD VNYRFIDYLV TLDEKM KWL ECGLDKNDYF LENMSIVMNS QDAVPFLLDP SSHMITVISN YYGNKTVLLS FLEEGFVKRL ENAVRFGSVV IIQDGEF FD PIISRLISRE FNHAGNRVTV EIGDHEVDVS GDFKLFIHSC DPSGDIPIFL RSRVRLVHFV TNKESIETRI FDITLTEE N AEMQRKREDL IKLNTEYRLK LKNLEKRLLE ELNNSQGNML ENDELMVTLN NLKKEAMNIE KKLSESEEFF PQFDNLVEE YSIIGKHSVK IFSMLEKFGQ FHWFYGISIG QFLSCFKRVF IKKSRETRAA RTRVDEILWL LYQEVYCQFS TALDKKFKMI MAMTMFCLY KFDIESEQYK EAVLTMIGVL SESSDGVPKL TVDTNDDLRY LWDYVTTKSY ISALNWFKNE FFVDEWNIAD V VANSENNY FTMASERDVD GTFKLIELAK ASKESLKIIP LGSIENLNYA QEEISKSKIE GGWILLQNIQ MSLSWVKTYL HK HVEETKA AEEHEKFKMF MTCHLTGDKL PAPLLQRTDR VVYEDIPGIL DTVKDLWGSQ FFTGKISGVW SVYCTFLLSW FHA LITART RLVPHGFSKK YYFNDCDFQF ASVYLENVLA TNSTNNIPWA QVRDHIATIV YGGKIDEEKD LEVVAKLCAH VFCG SDNLQ IVPGVRIPQP LLQQSEEEER ARLTAILSNT IEPADSLSSW LQLPRESILD YERLQAKEVA SSTEQLLQEM

UniProtKB: Dynein heavy chain, cytoplasmic

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

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

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

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / 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: 8
Details: 50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.75 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: EMDB MAP
EMDB ID:

23829

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119768
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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