[English] 日本語
Yorodumi
- PDB-3vaj: Structure of U2AF65 variant with BrU5C6 DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vaj
TitleStructure of U2AF65 variant with BrU5C6 DNA
Components
  • DNA (5'-D(*UP*UP*UP*UP*(BRU)P*CP*U)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/DNA / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / RNA BINDING PROTEIN / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsJenkins, J.L. / Kielkopf, C.L.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
Authors: Jenkins, J.L. / Agrawal, A.A. / Gupta, A. / Green, M.R. / Kielkopf, C.L.
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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*CP*U)-3')
E: DNA (5'-D(*UP*UP*UP*UP*(BRU)P*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,34318
Polymers42,2804
Non-polymers2,06314
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.869, 36.966, 99.992
Angle α, β, γ (deg.)90.000, 125.660, 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 / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 19075.754 Da / Num. of mol.: 2 / Fragment: RNA Binding Domains 1 and 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: PGEX-6P / 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*CP*U)-3')


Mass: 2064.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA

-
Non-polymers , 5 types, 241 molecules

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


Mass: 88.105 Da / Num. of mol.: 5 / 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.: 2 / 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.: 227 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38838 / % possible obs: 98.8 % / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.9-1.973.20.3563626192.6
1.97-2.053.40.3023812197.9
2.05-2.143.60.2473850199.8
2.14-2.253.70.20238991100
2.25-2.393.70.1673891199.9
2.39-2.583.70.1323911199.9
2.58-2.843.70.1073940199.9
2.84-3.253.60.0813919199.9
3.25-4.093.40.0613937199.1
4.09-503.50.0474053199.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→40.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.45 / SU B: 5.931 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 3658 9.9 %RANDOM
Rwork0.1911 ---
obs0.1954 37002 94.86 %-
all-40660 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.57 Å2 / Biso mean: 33.3794 Å2 / Biso min: 11.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å2-0.05 Å2
2---0.5 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 262 99 227 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223149
X-RAY DIFFRACTIONr_bond_other_d0.0010.022090
X-RAY DIFFRACTIONr_angle_refined_deg1.312.1144306
X-RAY DIFFRACTIONr_angle_other_deg1.07135109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86324.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84715461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0721514
X-RAY DIFFRACTIONr_chiral_restr0.110.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined0.1910.2569
X-RAY DIFFRACTIONr_nbd_other0.1930.22213
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21488
X-RAY DIFFRACTIONr_nbtor_other0.0850.21580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.219
X-RAY DIFFRACTIONr_mcbond_it0.7241.52215
X-RAY DIFFRACTIONr_mcbond_other0.1211.5713
X-RAY DIFFRACTIONr_mcangle_it0.81322755
X-RAY DIFFRACTIONr_scbond_it1.67331676
X-RAY DIFFRACTIONr_scangle_it2.3584.51550
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 240 -
Rwork0.237 2089 -
all-2329 -
obs--81.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41741.2635-0.2382.5617-0.81673.151-0.09490.0626-0.1936-0.13070.0033-0.06030.06520.12480.0916-0.1655-0.0123-0.0056-0.1759-0.0302-0.1065-11.29-19.633730.8386
26.84781.11550.12672.9726-0.4732.9648-0.06150.078-0.0236-0.13290.148-0.0426-0.17320.0425-0.0864-0.1312-0.04810.0239-0.1845-0.0331-0.0886-32.61785.655726.552
33.50331.753-0.1453.675-0.29793.1402-0.20920.17470.0328-0.28540.23520.08840.0586-0.2382-0.026-0.1567-0.0425-0.0359-0.14040.0193-0.141825.2318-27.725328.4487
46.34841.1941.423.133-0.80735.3249-0.11130.37850.0673-0.26190.0645-0.1729-0.1339-0.01690.0467-0.111-0.05760.005-0.09050.0073-0.20044.6658-4.06413.6885
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A143 - 237
2X-RAY DIFFRACTION2A258 - 336
3X-RAY DIFFRACTION3B143 - 237
4X-RAY DIFFRACTION4B258 - 336

+
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