[English] 日本語
Yorodumi
- PDB-4tu7: Structure of U2AF65 D231V variant with BrU5 DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tu7
TitleStructure of U2AF65 D231V variant with BrU5 DNA
Components
  • DNA (5'-D(*UP*UP*UP*UP*(BRU)P*UP*U)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA binding Protein/DNA / pre-mRNA splicing factor / RNA Recognition Motif / RNA binding Protein-DNA complex
Function / homology
Function and homology information


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / spliceosomal complex assembly / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / enzyme binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
U2 snRNP auxilliary factor, large subunit, splicing factor / RRM (RNA recognition motif) domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / DNA / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.087 Å
AuthorsAgrawal, A.A. / Jenkins, J.L. / Kielkopf, C.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA.
Authors: Agrawal, A.A. / McLaughlin, K.J. / Jenkins, J.L. / Kielkopf, C.L.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
B: Splicing factor U2AF 65 kDa subunit
P: DNA (5'-D(*UP*UP*UP*UP*(BRU)P*UP*U)-3')
E: DNA (5'-D(*UP*UP*UP*UP*(BRU)P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,40919
Polymers42,2504
Non-polymers2,15915
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-78 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.432, 37.361, 100.192
Angle α, β, γ (deg.)90.000, 125.600, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / DNA chain , 2 types, 4 molecules ABPE

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 19059.799 Da / Num. of mol.: 2 / Mutation: D231V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: pGEX-6p2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P26368
#2: DNA chain DNA (5'-D(*UP*UP*UP*UP*(BRU)P*UP*U)-3')


Mass: 2065.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 264 molecules

#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CPQ / N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE / DEOXY-BIGCHAP


Mass: 862.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H75N3O15 / Comment: detergent*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.96 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.6M AMMONIUM SULFATE, 10% DIOXANE, 0.1M MES PH 6.0, DEOXY-BIG CHAP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.087→39.447 Å / Num. obs: 28628 / % possible obs: 95.7 % / Redundancy: 3 % / Biso Wilson estimate: 33.58 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.044 / Rsym value: 0.037 / Net I/av σ(I): 16.634 / Net I/σ(I): 18.9 / Num. measured all: 86388
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.087-2.230.2283.21190139410.1540.2284.691
2.2-2.3330.1873.71190239430.1280.1876.296.4
2.33-2.493.10.1215.91161637720.0820.1218.797.5
2.49-2.693.10.0858.51089734990.0570.08512.197.5
2.69-2.952.90.05912.5926131400.040.05916.495.6
2.95-3.33.10.03620.3903229430.0240.0362597.6
3.3-3.812.90.02725.8735025420.0180.02735.394.9
3.81-4.6730.02230.7672522050.0150.02243.796.5
4.67-6.62.90.02130487916730.0140.02140.995
6.6-39.4472.90.01734.128259700.0110.01744.395.1

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.087→35.982 Å / FOM work R set: 0.8419 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 2824 9.9 %
Rwork0.1741 48064 -
obs0.1789 28628 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.83 Å2 / Biso mean: 35.11 Å2 / Biso min: 15.76 Å2
Refinement stepCycle: final / Resolution: 2.087→35.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 262 386 249 3581
Biso mean--42.88 40.16 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073170
X-RAY DIFFRACTIONf_angle_d1.2084337
X-RAY DIFFRACTIONf_chiral_restr0.046476
X-RAY DIFFRACTIONf_plane_restr0.005515
X-RAY DIFFRACTIONf_dihedral_angle_d16.5221278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.087-2.11080.3213950.26061015111058
2.1108-2.13560.31341840.23081650183497
2.1356-2.16170.28931670.20721691185896
2.1617-2.1890.27221620.20611687184995
2.189-2.21780.2581920.21381650184295
2.2178-2.24820.27971740.21121543171793
2.2482-2.28030.26411810.19461637181892
2.2803-2.31440.23191840.20431615179992
2.3144-2.35050.27641680.20641555172390
2.3505-2.38910.27921580.20081585174394
2.3891-2.43020.24212030.19781685188896
2.4302-2.47440.25131950.18981675187096
2.4744-2.5220.28951680.20351639180797
2.522-2.57350.26322190.19421620183996
2.5735-2.62940.25991720.18921658183093
2.6294-2.69060.26421800.19091627180793
2.6906-2.75780.25041660.18451539170592
2.7578-2.83240.22361900.18671608179892
2.8324-2.91570.30221710.19751566173790
2.9157-3.00970.21331830.19011620180395
3.0097-3.11720.24142170.17941677189496
3.1172-3.2420.25381820.18251594177695
3.242-3.38940.2171980.1721666186496
3.3894-3.5680.19811630.15981583174692
3.568-3.79130.19991760.15161548172489
3.7913-4.08360.18341850.13681618180394
4.0836-4.49390.1631630.14091625178894
4.4939-5.14260.191640.14581683184795
5.1426-6.47290.21441630.18271556171990
6.4729-35.98780.17631610.17131649181093

+
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