[English] 日本語
Yorodumi
- PDB-3p5t: CFIm25-CFIm68 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p5t
TitleCFIm25-CFIm68 complex
Components
  • Cleavage and polyadenylation specificity factor subunit 5
  • Cleavage and polyadenylation specificity factor subunit 6
KeywordsRNA BINDING PROTEIN / RRM domain / Poly(A) site recognition / RNA / nuclear
Function / homology
Function and homology information


exon-exon junction complex binding / positive regulation of pro-B cell differentiation / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation ...exon-exon junction complex binding / positive regulation of pro-B cell differentiation / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / positive regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / mRNA 3'-end processing / paraspeckles / RNA Polymerase II Transcription Termination / post-transcriptional regulation of gene expression / protein heterotetramerization / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / Signaling by FGFR1 in disease / protein tetramerization / centriolar satellite / histone deacetylase binding / mRNA processing / cell differentiation / nuclear speck / nuclear body / ribonucleoprotein complex / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / RRM (RNA recognition motif) domain / NUDIX hydrolase-like domain superfamily ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / RRM (RNA recognition motif) domain / NUDIX hydrolase-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cleavage and polyadenylation specificity factor subunit 5 / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, H. / Tong, S. / Li, X. / Shi, H. / Gao, Y. / Ge, H. / Niu, L. / Teng, M.
CitationJournal: To be Published
Title: Structural basis of pre-mRNA recognition by the human cleavage factor Im complex
Authors: Li, H. / Tong, S. / Li, X. / Shi, H. / Gao, Y. / Ge, H. / Niu, L. / Teng, M.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 5
B: Cleavage and polyadenylation specificity factor subunit 5
C: Cleavage and polyadenylation specificity factor subunit 5
D: Cleavage and polyadenylation specificity factor subunit 5
E: Cleavage and polyadenylation specificity factor subunit 5
F: Cleavage and polyadenylation specificity factor subunit 5
L: Cleavage and polyadenylation specificity factor subunit 6
M: Cleavage and polyadenylation specificity factor subunit 6
N: Cleavage and polyadenylation specificity factor subunit 6
O: Cleavage and polyadenylation specificity factor subunit 6
P: Cleavage and polyadenylation specificity factor subunit 6
Q: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)202,58112
Polymers202,58112
Non-polymers00
Water4,468248
1
A: Cleavage and polyadenylation specificity factor subunit 5
B: Cleavage and polyadenylation specificity factor subunit 5
L: Cleavage and polyadenylation specificity factor subunit 6
M: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers67,5274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cleavage and polyadenylation specificity factor subunit 5
D: Cleavage and polyadenylation specificity factor subunit 5
N: Cleavage and polyadenylation specificity factor subunit 6
O: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers67,5274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cleavage and polyadenylation specificity factor subunit 5
F: Cleavage and polyadenylation specificity factor subunit 5
P: Cleavage and polyadenylation specificity factor subunit 6
Q: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers67,5274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.440, 105.690, 147.080
Angle α, β, γ (deg.)90.00, 112.72, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Cleavage and polyadenylation specificity factor subunit 5 / Cleavage factor Im 25 / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 ...Cleavage factor Im 25 / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Nucleoside diphosphate-linked moiety X motif 21 / Nudix motif 21 / Pre-mRNA cleavage factor Im 25 kDa subunit


Mass: 23614.115 Da / Num. of mol.: 6 / Fragment: UNP residues 34-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT21, CFIM25, CPSF25, CPSF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O43809
#2: Protein
Cleavage and polyadenylation specificity factor subunit 6 / Cleavage factor Im 68 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CF Im68 / ...Cleavage factor Im 68 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CF Im68 / CPSF 68 kDa subunit / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 10149.415 Da / Num. of mol.: 6 / Fragment: UNP residues 80-161 / Mutation: C159S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF6, CFIM68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16630
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% PEG 3350, 5% dioxane, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 3, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 62054 / Num. obs: 58226 / % possible obs: 98.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.768 Å / % possible all: 98.92

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.4.0067refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CL3, 2FY1

2cl3

2fy1


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26543 3101 5.1 %RANDOM
Rwork0.21369 ---
all0.22 62054 --
obs0.21632 58226 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.363 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å2-1.44 Å2
2---2.32 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13005 0 0 248 13253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213354
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.96618188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0651639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2924.149605
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.796152117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5461567
X-RAY DIFFRACTIONr_chiral_restr0.0940.22008
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110259
X-RAY DIFFRACTIONr_mcbond_it0.5351.58246
X-RAY DIFFRACTIONr_mcangle_it0.994213262
X-RAY DIFFRACTIONr_scbond_it1.02135108
X-RAY DIFFRACTIONr_scangle_it1.8024.54926
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 227 -
Rwork0.362 4208 -
obs--99.35 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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