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- EMDB-7113: Cryo-EM structure of human CPSF-160-WDR33 complex at 3.36A resolution -

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Basic information

Entry
Database: EMDB / ID: 7113
TitleCryo-EM structure of human CPSF-160-WDR33 complex at 3.36A resolution
Map dataHuman CPSF160-WDR33 complex
SampleBinary complex of human CPSF-160-WDR33
  • Cleavage and polyadenylation specificity factor subunit 1
  • pre-mRNA 3' end processing protein WDR33
Function / homologyWD40 repeat / tRNA processing in the nucleus / Trp-Asp (WD) repeats profile. / CPSF A subunit region / WD domain, G-beta repeat / WD40-repeat-containing domain superfamily / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage of Growing Transcript in the Termination Region ...WD40 repeat / tRNA processing in the nucleus / Trp-Asp (WD) repeats profile. / CPSF A subunit region / WD domain, G-beta repeat / WD40-repeat-containing domain superfamily / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage of Growing Transcript in the Termination Region / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA Splicing - Major Pathway / mRNA 3'-end processing / Processing of Intronless Pre-mRNAs / Trp-Asp (WD) repeats circular profile. / mRNA 3'-UTR AU-rich region binding / mRNA cleavage and polyadenylation specificity factor complex / pre-mRNA cleavage required for polyadenylation / postreplication repair / mRNA 3'-end processing / collagen trimer / mRNA cleavage / termination of RNA polymerase II transcription / mRNA export from nucleus / mRNA polyadenylation / fibrillar center / mRNA splicing, via spliceosome / spermatogenesis / enzyme binding / RNA binding / nucleoplasm / nucleus / Cleavage and polyadenylation specificity factor subunit 1 / pre-mRNA 3' end processing protein WDR33
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.36 Å resolution
AuthorsSun Y / Zhang Y
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Molecular basis for the recognition of the human AAUAAA polyadenylation signal.
Authors: Yadong Sun / Yixiao Zhang / Keith Hamilton / James L Manley / Yongsheng Shi / Thomas Walz / Liang Tong
Validation ReportPDB-ID: 6bly

SummaryFull reportAbout validation report
DateDeposition: Nov 12, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Feb 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bly
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7113.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.07 Å/pix.
= 205.44 Å
192 pix
1.07 Å/pix.
= 205.44 Å
192 pix
1.07 Å/pix.
= 205.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.20371085 - 0.36129674
Average (Standard dev.)5.5061046E-6 (0.014194904)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 205.44 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z205.440205.440205.440
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.2040.3610.000

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Supplemental data

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Sample components

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Entire Binary complex of human CPSF-160-WDR33

EntireName: Binary complex of human CPSF-160-WDR33 / Number of components: 3
MassExperimental: 225 kDa

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Component #1: protein, Binary complex of human CPSF-160-WDR33

ProteinName: Binary complex of human CPSF-160-WDR33 / Recombinant expression: No
MassExperimental: 225 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Cleavage and polyadenylation specificity factor subunit 1

ProteinName: Cleavage and polyadenylation specificity factor subunit 1
Recombinant expression: No
MassTheoretical: 161.074234 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, pre-mRNA 3' end processing protein WDR33

ProteinName: pre-mRNA 3' end processing protein WDR33 / Recombinant expression: No
MassTheoretical: 67.546812 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.18 mg/ml
Buffer solution: 25 mM Tris-HCl, pH 7.9, 380 mM NaCl, 5mM DTT
pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / 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: 70 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 225000 X (nominal), 46729 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2468

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 456310
3D reconstructionSoftware: RELION / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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