[English] 日本語
Yorodumi
- PDB-3q2t: Crystal Structure of CFIm68 RRM/CFIm25/RNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q2t
TitleCrystal Structure of CFIm68 RRM/CFIm25/RNA complex
Components
  • Cleavage and polyadenylation specificity factor subunit 5
  • Cleavage and polyadenylation specificity factor subunit 6
  • RNA
KeywordsRNA BINDING PROTEIN/RNA / CFIm / CFIm25 / CFIm68 / CPSF5 / CPSF6 / CPSF / 3' end processing / RNA processing / cleavage factor / Nudix protein / protein-protein complex / protein-RNA complex / RRM / nudix fold / RNA BINDING PROTEIN-RNA complex
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
RNA / Cleavage and polyadenylation specificity factor subunit 5 / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.061 Å
AuthorsYang, Q. / Coseno, M. / Gilmartin, G.M. / Doublie, S.
CitationJournal: Structure / Year: 2011
Title: Crystal Structure of a Human Cleavage Factor CFI(m)25/CFI(m)68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping.
Authors: Yang, Q. / Coseno, M. / Gilmartin, G.M. / Doublie, S.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 6
D: Cleavage and polyadenylation specificity factor subunit 6
E: RNA
F: RNA


Theoretical massNumber of molelcules
Total (without water)100,1296
Polymers100,1296
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.406, 138.406, 138.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein Cleavage and polyadenylation specificity factor subunit 5 / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Nucleoside ...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: 24030.703 Da / Num. of mol.: 2 / Fragment: residues 21-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFIM25, CPSF25, CPSF5, NUDT21 / Plasmid: His6-MBP fusion vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: O43809
#2: Protein Cleavage and polyadenylation specificity factor subunit 6 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 24485.863 Da / Num. of mol.: 2 / Fragment: RRM domain, residues 13-235 / Mutation: C159V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFIM68, CPSF6 / Plasmid: pET22 C-terminal His6 tag / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q16630
#3: RNA chain RNA


Mass: 1547.952 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized by Dharmacon
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2M Magnesium Formate, 0.05M HEPES pH 7.0, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 23, 2010 / Details: mirrors
RadiationMonochromator: MAR mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.033
ReflectionResolution: 3.06→20 Å / Num. all: 16919 / Num. obs: 16919 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 36.8 % / Rmerge(I) obs: 0.146 / Χ2: 0.998 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.06-3.1727.50.999916341.024100
3.17-3.330.80.92616861.001100
3.3-3.4432.60.6116791100
3.44-3.6334.20.47516700.998100
3.63-3.8535.70.35816831.005100
3.85-4.15370.21616780.992100
4.15-4.5638.50.15816871.002100
4.56-5.2141.30.1091696199.9
5.21-6.5244.80.11217220.996100
6.52-2044.40.05317840.978100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BHO

3bho


Resolution: 3.061→19.977 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.786
Cross valid method: Throughout. Twin based reflections are in the same set
σ(F): 0.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 1548 5.67 %Random
Rwork0.2108 ---
obs0.2137 16919 84.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.161 Å2 / ksol: 0.233 e/Å3
Displacement parametersBiso max: 153.66 Å2 / Biso mean: 64.4604 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 3.061→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 204 0 3 5025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065178
X-RAY DIFFRACTIONf_angle_d0.9667064
X-RAY DIFFRACTIONf_chiral_restr0.059776
X-RAY DIFFRACTIONf_plane_restr0.003880
X-RAY DIFFRACTIONf_dihedral_angle_d17.4481958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.061-3.18260.50411150.29562263237864
3.1826-3.32680.32341540.27612922307680
3.3268-3.50120.34461590.25942881304081
3.5012-3.7190.36171520.24172875302780
3.719-4.00380.33881360.20972738287478
4.0038-4.40230.27931510.18142928307981
4.4023-5.02930.21741530.1772961311483
5.0293-6.29890.30651520.20953083323586
6.2989-19.19380.22521830.19113270345392

+
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