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- EMDB-3908: PolyA polymerase module of the cleavage and polyadenylation facto... -

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Basic information

Entry
Database: EMDB / ID: 3908
TitlePolyA polymerase module of the cleavage and polyadenylation factor (CPF) from Saccharomyces cerevisiae
SampleComplex of Cft1, Yth1, Pfs2 and Fip1
SourceSaccharsaccharomyces cerevisiae (strain atcc 204508 / s288c)omyces
Map data
Methodsingle particle reconstruction, at 3.55 Å resolution
AuthorsCasanal A / Kumar A
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 ReportPDB-ID: 6eoj

SummaryFull reportAbout validation report
DateDeposition: Oct 9, 2017 / Header (metadata) release: Nov 15, 2017 / Map release: Nov 15, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.15
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6eoj
  • Surface level: 0.15
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_3908.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.4 Å/pix.
= 224. Å
160 pix
1.4 Å/pix.
= 224. Å
160 pix
1.4 Å/pix.
= 224. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.15 (by author), 0.15 (movie #1):
Minimum - Maximum-0.55501544 - 0.8373203
Average (Standard dev.)0.00017478284 (0.031612962)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 224 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z224.000224.000224.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.5550.8370.000

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Supplemental data

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Mask #1

Fileemd_3908_msk_1.map ( map file in CCP4 format, 16385 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3908_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Complex of Cft1, Yth1, Pfs2 and Fip1

EntireName: Complex of Cft1, Yth1, Pfs2 and Fip1 / Number of components: 5
MassTheoretical: 270 kDa

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Component #1: protein, Complex of Cft1, Yth1, Pfs2 and Fip1

ProteinName: Complex of Cft1, Yth1, Pfs2 and Fip1 / Recombinant expression: No
MassTheoretical: 270 kDa
SourceSpecies: Saccharsaccharomyces cerevisiae (strain atcc 204508 / s288c)omyces
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #2: protein, Protein CFT1

ProteinName: Protein CFT1 / Recombinant expression: No
MassTheoretical: 153.577156 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #3: protein, mRNA 3'-end-processing protein YTH1

ProteinName: mRNA 3'-end-processing protein YTH1 / Recombinant expression: No
MassTheoretical: 24.560416 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #4: protein, Polyadenylation factor subunit 2,Polyadenylation factor ...

ProteinName: Polyadenylation factor subunit 2,Polyadenylation factor subunit 2
Recombinant expression: No
MassTheoretical: 53.636645 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Strain: ATCC 204508 / S288c

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Component #5: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: OTHER
LensMagnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4227

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 77197
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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