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- PDB-5vh9: Cryo-EM structure of yeast cytoplasmic dynein-1 with Lis1 and ATP -

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Basic information

Entry
Database: PDB / ID: 5vh9
TitleCryo-EM structure of yeast cytoplasmic dynein-1 with Lis1 and ATP
DescriptorDynein heavy chain
cytoplasmic
Nuclear distribution protein PAC1
KeywordsMOTOR PROTEIN / cytoplasmic dynein / lis1
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (7.7 Å resolution / Particle / Single particle)
AuthorsCianfrocco, M.A. / DeSantis, M.E. / Htet, Z.M. / Tran, P.T. / Reck-Peterson, S.L. / Leschziner, A.E.
CitationCell, 2017, 170, 1197-1208.e12

Cell, 2017, 170, 1197-1208.e12 Yorodumi Papers
Lis1 Has Two Opposing Modes of Regulating Cytoplasmic Dynein.
Morgan E DeSantis / Michael A Cianfrocco / Zaw Min Htet / Phuoc Tien Tran / Samara L Reck-Peterson / Andres E Leschziner

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2017 / Release: Sep 6, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 6, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Sep 27, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: Dynein heavy chain, cytoplasmic
B: Nuclear distribution protein PAC1


Theoretical massNumber of molelcules
Total (without water)313,3122
Polyers313,3122
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)520
ΔGint (kcal/M)-3
Surface area (Å2)124590

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Components

#1: Polypeptide(L)Dynein heavy chain, cytoplasmic / Dynein heavy chain / cytosolic / DYHC / Cytoplasmic dynein-1


Mass: 272666.250 Da / Num. of mol.: 1 / Fragment: UNP residues 1448-3028,3298-4092
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P36022

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Nuclear distribution protein PAC1 / Lissencephaly-1 homolog / LIS-1 / nudF homolog / Lis1


Mass: 40645.449 Da / Num. of mol.: 1 / Fragment: UNP residues 140-493
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: A6ZPA6

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Dynein-Lis1 co-complex with ATP / Type: COMPLEX / Entity ID: 1,2 / Source: RECOMBINANT
Molecular weightValue: 0.444 deg. / Units: MEGADALTONS / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae
Source (recombinant)Organism: Saccharomyces cerevisiae / Plasmid: RPY1302
Buffer solutionpH: 8
SpecimenConc.: 0.23 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: No pretreatment of grids / Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil UltrAuFoil 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 276 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.15 sec. / Electron dose: 82 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 2 / Number of real images: 5614
Image scansMovie frames/image: 53 / Used frames/image: 3-53

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Processing

EM software
IDNameVersionCategoryDetailsImaging IDFitting ID
2Leginon3.2IMAGE ACQUISITIONAutomated hole and exposure targeting1
7UCSF Chimera1.11.2MODEL FITTINGInitial docking of atomic coordinates was performed in Chimera.1
13Rosetta3.7MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 25520 / Symmetry type: POINT
Atomic model buildingOverall b value: 50 / Ref protocol: FLEXIBLE FIT / Ref space: REAL

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