[English] 日本語
Yorodumi
- PDB-9c7b: Crystal structure of R150H neurodevelopmental disease-associated ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c7b
TitleCrystal structure of R150H neurodevelopmental disease-associated U2AF2 variant
Components
  • DNA/RNA (5'-R(P*UP*U)-D(P*U)-R(P*UP*U)-D(P*(BRU))-R(P*CP*C)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/RNA/DNA / PROTEIN-RNA COMPLEX / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN-RNA COMPLEX / RNA BINDING PROTEIN-SPLICING complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-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 / 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
Similarity search - Domain/homology
DNA/RNA hybrid / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsMaji, D. / Jenkins, J.L. / Kielkopf, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070503-15 United States
CitationJournal: Biochemistry / Year: 2024
Title: Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions.
Authors: Maji, D. / Jenkins, J.L. / Boutz, P.L. / Kielkopf, C.L.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
B: DNA/RNA (5'-R(P*UP*U)-D(P*U)-R(P*UP*U)-D(P*(BRU))-R(P*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)24,6682
Polymers24,6682
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-17 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.722, 55.793, 76.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 22218.281 Da / Num. of mol.: 1 / Mutation: R150H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: PGEX-6P / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26368
#2: DNA/RNA hybrid DNA/RNA (5'-R(P*UP*U)-D(P*U)-R(P*UP*U)-D(P*(BRU))-R(P*CP*C)-3')


Mass: 2449.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24 M sodium malonate pH 7.0, 5% w/v sucrose, 25% w/v PEG 3350, with addition of 0.1 uL of 5% w/v LDAO detergent

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→38.34 Å / Num. obs: 69899 / % possible obs: 98.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 11.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1611 / CC1/2: 0.852 / Rpim(I) all: 0.219 / % possible all: 82.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
PHENIX1.20.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6XLW

6xlw


Resolution: 1.4→37.98 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 15.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1671 4636 6.63 %
Rwork0.1344 65263 -
obs0.1366 69899 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.65 Å2 / Biso mean: 23.1792 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: final / Resolution: 1.4→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 160 0 248 1924
Biso mean---31.5 -
Num. residues----209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.410.26881280.22991695182376
1.41-1.430.22751430.19661959210288
1.43-1.450.2391440.18232082222693
1.45-1.470.20561320.15812175230797
1.47-1.490.21771590.15392148230798
1.49-1.510.19921630.13942228239197
1.51-1.530.18691540.13882143229799
1.53-1.550.20471420.13012255239799
1.55-1.570.14331550.12372167232298
1.57-1.60.17851700.13012185235599
1.6-1.630.14941550.12412173232897
1.63-1.660.18631620.11772218238099
1.66-1.690.17191540.11472224237898
1.69-1.720.16511650.113821652330100
1.72-1.760.17421720.11732209238198
1.76-1.80.15521450.12212211235699
1.8-1.850.13071330.11962208234199
1.85-1.90.1871970.12512203240099
1.9-1.950.1991640.12222169233399
1.95-2.020.15251370.11872240237799
2.02-2.090.16341340.121222542388100
2.09-2.170.18521380.11432207234599
2.17-2.270.14681610.11842240240199
2.27-2.390.17541530.115422022355100
2.39-2.540.15961720.1312222239499
2.54-2.740.161700.135922122382100
2.74-3.010.151410.141622132354100
3.01-3.450.15921700.138122242394100
3.45-4.340.14231630.12922224238799
4.34-37.980.17871600.175122082368100

+
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