[English] 日本語
Yorodumi
- EMDB-7114: Cryo-EM structure of human CPSF-160-WDR33 complex at 3.8 A resolution -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7114
TitleCryo-EM structure of human CPSF-160-WDR33 complex at 3.8 A resolution
Map dataHuman CPSF160-WDR33 complex at 3.8 A resolution
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 3'-end processing / mRNA Splicing - Major Pathway / Processing of Intronless Pre-mRNAs / Trp-Asp (WD) repeats circular profile. / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-UTR AU-rich region binding / pre-mRNA cleavage required for polyadenylation / postreplication repair / mRNA 3'-end processing / collagen trimer / 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 / 3.8 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: 6bm0

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

-
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-6bm0
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_7114.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-0.1357154 - 0.25742173
Average (Standard dev.)-0.000044293636 (0.010230549)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.00.00.0
Limit191.0191.0191.0
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-0.1360.257-0.000

-
Supplemental data

-
Sample components

-
Entire Binary complex of human CPSF-160-WDR33

EntireName: Binary complex of human CPSF-160-WDR33
Details: WDR33 is bound between the top faces of b- propeller A and C in CPSF-160
Number of components: 3

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

ProteinName: Binary complex of human CPSF-160-WDR33
Details: WDR33 is bound between the top faces of b- propeller A and C in CPSF-160
Recombinant expression: No
MassExperimental: 225 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

-
Component #2: 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)

-
Component #3: 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)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.8 mg/ml
Buffer solution: 25 mM Tris-HCl, pH 7.9, 300 mM NaCl, 5 mM DTT
pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
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: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 225000.0 X (nominal), 38462.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1300.0 - 2700.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1625

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 205373
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more