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- PDB-6eoj: PolyA polymerase module of the cleavage and polyadenylation facto... -

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Basic information

Database: PDB / ID: 6eoj
TitlePolyA polymerase module of the cleavage and polyadenylation factor (CPF) from Saccharomyces cerevisiae
DescriptorProtein CFT1
mRNA 3'-end-processing protein YTH1
Polyadenylation factor subunit 2
KeywordsRNA BINDING PROTEIN / WD40 / Beta-propeller / Zinc finger / 3'end processing
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Saccharomyces cerevisiae s288c / yeast / Baker's yeast / image: Saccharomyces cerevisiae
MethodElectron microscopy (3.55 Å resolution / Particle / Single particle)
AuthorsCasanal, A. / Kumar, A. / Hill, C.H. / Emsley, P. / Passmore, L.
CitationScience, 2017, 358, 1056-1059

Science, 2017, 358, 1056-1059 Yorodumi Papers
Architecture of eukaryotic mRNA 3'-end processing machinery.
Ana Casañal / Ananthanarayanan Kumar / Chris H Hill / Ashley D Easter / Paul Emsley / Gianluca Degliesposti / Yuliya Gordiyenko / Balaji Santhanam / Jana Wolf / Katrin Wiederhold / Gillian L Dornan / Mark Skehel / Carol V Robinson / Lori A Passmore

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 9, 2017 / Release: Nov 15, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 15, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Deposited unit
A: Protein CFT1
B: mRNA 3'-end-processing protein YTH1
D: Polyadenylation factor subunit 2,Polyadenylation factor subunit 2
hetero molecules

Theoretical massNumber of molelcules
Total (without water)231,9055

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)13370
ΔGint (kcal/M)-63
Surface area (Å2)56480


#1: Polypeptide(L)Protein CFT1 / Cleavage factor two protein 1

Mass: 153577.156 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
References: UniProt: Q06632
#2: Polypeptide(L)mRNA 3'-end-processing protein YTH1 / Yeast 30 kDa homolog 1

Mass: 24560.416 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
References: UniProt: Q06102
#3: Polypeptide(L)Polyadenylation factor subunit 2,Polyadenylation factor subunit 2

Mass: 53636.645 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / , (gene. exp.) Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
References: UniProt: P42841
#4: ChemicalChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Complex of Cft1, Yth1, Pfs2 and Fip1 / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightValue: 0.27 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: SaccharSaccharomyces cerevisiae (strain ATCC 204508 / S288c)omyces
Source (recombinant)Organism: Spodoptera frugiperda
Buffer solutionpH: 7.9
Buffer component
IDConc.UnitsNameBuffer ID
2150mMSodium Chloride1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 16 sec. / Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 5 / Number of real images: 4227
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansMovie frames/image: 20


EM software
IDNameVersionCategoryImage processing IDImaging IDDetailsFitting ID
Particle selectionNumber of particles selected: 460167
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 77197 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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