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- EMDB-7112: Cryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex... -

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Basic information

Entry
Database: EMDB / ID: 7112
TitleCryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex at 3.4 A resolution
Map dataHuman CPSF160-WDR33-CPSF30-PAS complex at 3.4 A resolution
SampleQuaternary complex of human CPSF-160-WDR33-CPSF-30 with AAUAAA polyadenylation signal
  • CPSF-160-WDR33
  • CPSF-30Cleavage and polyadenylation specificity factor
  • AAUAAA polyadenylation signal
  • (Cleavage and polyadenylation specificity factor subunit ...) x 2
  • pre-mRNA 3' end processing protein WDR33
  • nucleic-acidNucleic acid
  • ligand
Function / homologyCleavage/polyadenylation specificity factor, A subunit, C-terminal / Trp-Asp (WD) repeats circular profile. / Zinc finger C3H1-type profile. / Trp-Asp (WD) repeats profile. / CPSF A subunit region / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WD domain, G-beta repeat / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCCH-type superfamily ...Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Trp-Asp (WD) repeats circular profile. / Zinc finger C3H1-type profile. / Trp-Asp (WD) repeats profile. / CPSF A subunit region / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WD domain, G-beta repeat / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCCH-type superfamily / WD40-repeat-containing domain superfamily / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / Zinc finger, CCHC-type / WD40 repeat / Zinc finger, CCCH-type / Cleavage of Growing Transcript in the Termination Region / Zinc finger CCHC-type profile. / mRNA Splicing - Major Pathway / Processing of Intronless Pre-mRNAs / Transport of Mature mRNA Derived from an Intronless Transcript / Inhibition of Host mRNA Processing and RNA Silencing / tRNA processing in the nucleus / mRNA 3'-end processing / modification by virus of host mRNA processing / 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 / endoribonuclease activity / mRNA polyadenylation / fibrillar center / mRNA splicing, via spliceosome / spermatogenesis / intracellular membrane-bounded organelle / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / Cleavage and polyadenylation specificity factor subunit 4 / Cleavage and polyadenylation specificity factor subunit 1 / pre-mRNA 3' end processing protein WDR33
Function and homology information
SourceHomo sapiens (human) / Simian virus 40
Methodsingle particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsSun Y / Zhang Y / Hamilton K / Walz T / Tong L
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: 6dnh

SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Jun 27, 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
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  • Surface view with fitted model
  • Atomic models: : PDB-6dnh
  • 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_7112.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-0.17654768 - 0.31463027
Average (Standard dev.)0.00002113147 (0.013521084)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.0.0.
Limit191.191.191.
Spacing192192192
CellA=B=C: 205.44 Å
α=β=γ: 90.0 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-0.1770.3150.000

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Supplemental data

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Sample components

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Entire Quaternary complex of human CPSF-160-WDR33-CPSF-30 with AAUAAA po...

EntireName: Quaternary complex of human CPSF-160-WDR33-CPSF-30 with AAUAAA polyadenylation signal
Number of components: 9

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Component #1: protein, Quaternary complex of human CPSF-160-WDR33-CPSF-30 with ...

ProteinName: Quaternary complex of human CPSF-160-WDR33-CPSF-30 with AAUAAA polyadenylation signal
Recombinant expression: No
MassExperimental: 255 kDa

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Component #2: protein, CPSF-160-WDR33

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

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Component #3: protein, CPSF-30

ProteinName: CPSF-30Cleavage and polyadenylation specificity factor
Recombinant expression: No
MassTheoretical: 27 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, AAUAAA polyadenylation signal

ProteinName: AAUAAA polyadenylation signal / Recombinant expression: No
MassTheoretical: 5 kDa
SourceSpecies: Simian virus 40

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Component #5: protein, Cleavage and polyadenylation specificity factor subunit 1

ProteinName: Cleavage and polyadenylation specificity factor subunit 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 161.074234 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: protein, pre-mRNA 3' end processing protein WDR33

ProteinName: pre-mRNA 3' end processing protein WDR33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.546812 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: protein, Cleavage and polyadenylation specificity factor subunit 4

ProteinName: Cleavage and polyadenylation specificity factor subunit 4
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.646055 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: nucleic-acid, RNA (5'-R(P*AP*AP*UP*AP*AP*AP*C)-3')

Nucleic-acidName: RNA (5'-R(P*AP*AP*UP*AP*AP*AP*C)-3') / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AACCUCCAAU AAACAAC
MassTheoretical: 5.361317 kDa
SourceSpecies: Simian virus 40

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Component #9: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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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, 5 mM 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: 7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 225000. X (nominal), 46729. X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (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: 173632
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Input PDB model: 2RHK
Chain ID: C
Output model

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