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- EMDB-27811: Symmetry expansion of yeast cytoplasmic dynein-1 bound to Lis1 in... -

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Entry
Database: EMDB / ID: EMD-27811
TitleSymmetry expansion of yeast cytoplasmic dynein-1 bound to Lis1 in the chi conformation.
Map data
Sample
  • Complex: cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation
    • Protein or peptide: Dynein heavy chain, cytoplasmic
    • Protein or peptide: Nuclear distribution protein PAC1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsdynein / motor protein / transport
Function / homology
Function and homology information


positive regulation of microtubule plus-end binding / microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / vesicle transport along microtubule / Antigen processing: Ubiquitination & Proteasome degradation / dynein complex / microtubule plus-end binding / minus-end-directed microtubule motor activity / dynein light intermediate chain binding ...positive regulation of microtubule plus-end binding / microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / vesicle transport along microtubule / Antigen processing: Ubiquitination & Proteasome degradation / dynein complex / microtubule plus-end binding / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / nuclear migration / microtubule associated complex / dynein intermediate chain binding / dynein complex binding / microtubule-based movement / establishment of mitotic spindle orientation / cytoplasmic microtubule / kinetochore / spindle pole / nuclear envelope / microtubule / cell division / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain ...Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / 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
Similarity search - Domain/homology
Dynein heavy chain, cytoplasmic / Nuclear distribution protein PAC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsReimer JM / Lahiri I / Leschziner AE
Funding support United States, 2 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2370-19 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM107214 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Lis1 relieves cytoplasmic dynein-1 autoinhibition by acting as a molecular wedge.
Authors: Eva P Karasmanis / Janice M Reimer / Agnieszka A Kendrick / Kendrick H V Nguyen / Jennifer A Rodriguez / Joey B Truong / Indrajit Lahiri / Samara L Reck-Peterson / Andres E Leschziner /
Abstract: Cytoplasmic dynein-1 transports intracellular cargo towards microtubule minus ends. Dynein is autoinhibited and undergoes conformational changes to form an active complex that consists of one or two ...Cytoplasmic dynein-1 transports intracellular cargo towards microtubule minus ends. Dynein is autoinhibited and undergoes conformational changes to form an active complex that consists of one or two dynein dimers, the dynactin complex, and activating adapter(s). The Lissencephaly 1 gene, LIS1, is genetically linked to the dynein pathway from fungi to mammals and is mutated in people with the neurodevelopmental disease lissencephaly. Lis1 is required for active dynein complexes to form, but how it enables this is unclear. Here, we present a structure of two yeast dynein motor domains with two Lis1 dimers wedged in-between. The contact sites between dynein and Lis1 in this structure, termed 'Chi,' are required for Lis1's regulation of dynein in Saccharomyces cerevisiae in vivo and the formation of active human dynein-dynactin-activating adapter complexes in vitro. We propose that this structure represents an intermediate in dynein's activation pathway, revealing how Lis1 relieves dynein's autoinhibited state.
History
DepositionAug 8, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27811.png

Downloads & links

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Map

FileDownload / File: emd_27811.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.879
Minimum - Maximum-1.4162124 - 3.022418
Average (Standard dev.)0.0030956923 (±0.09063895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 461.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27811_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_27811_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation

EntireName: cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation
Components
  • Complex: cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation
    • Protein or peptide: Dynein heavy chain, cytoplasmic
    • Protein or peptide: Nuclear distribution protein PAC1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation

SupramoleculeName: cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Dynein heavy chain, cytoplasmic

MacromoleculeName: Dynein heavy chain, cytoplasmic / type: protein_or_peptide / ID: 1 / Details: 100% identical to UniParc UPI0005D9E17C / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 331.524 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 VLFCDQINLP 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: Nuclear distribution protein PAC1

MacromoleculeName: Nuclear distribution protein PAC1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 57.030617 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GMTNWQQQLP LTDTQKNELD KSVLRYLNWN YKQTVRHEHA QDYESVRHAI VTLSGFLLQE SVDRQEFISN NDTSNESMVD IDELLLPKK WNSIVRLQKK IIELEQNTET LVSQIKDLNT QVSELAQFKP TTSNGTSAHN VLKWIPRNLP SCLINVESSV T SVKLHPNL ...String:
GMTNWQQQLP LTDTQKNELD KSVLRYLNWN YKQTVRHEHA QDYESVRHAI VTLSGFLLQE SVDRQEFISN NDTSNESMVD IDELLLPKK WNSIVRLQKK IIELEQNTET LVSQIKDLNT QVSELAQFKP TTSNGTSAHN VLKWIPRNLP SCLINVESSV T SVKLHPNL PIVFVATDHG KLYAFDLFNY TIPLASLQSH TKAITSMDVL FTNYTNSSKK NYLVIVTASK DLQIHVFKWV SE ECKFQQI RSLLGHEHIV SAVKIWQKNN DVHIASCSRD QTVKIWDFHN GWSLKTFQPH SQWVRSIDVL GDYIISGSHD TTL RLTHWP SGNGLSVGTG HEFPIEKVKF IHFIEDSPEI RFRTPSTDRY KNWGMQYCVS ASRDRTIKIW EIPLPTLMAH RAPI PNPTD SNFRCVLTLK GHLSWVRDIS IRGQYLFSCA DDKSVRCWDL NTGQCLHVWE KLHTGFVNCL DLDVDFDSNV TPRQM MVTG GLDCKSNVFM R

UniProtKB: Nuclear distribution protein PAC1

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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: 7.4
VitrificationCryogen name: ETHANE
Detailsstreptavidin affinity grids were used

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 2.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7mgm

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46770
FSC plot (resolution estimation)

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