[English] 日本語
Yorodumi
- PDB-5oem: Crystal Structure of Interferon Regulatory Factor 9 IAD Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oem
TitleCrystal Structure of Interferon Regulatory Factor 9 IAD Domain
ComponentsInterferon regulatory factor 9
KeywordsTRANSCRIPTION / IRF9
Function / homology
Function and homology information


Interferon alpha/beta signaling / immune system process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Interferon regulatory factor 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRengachari, S. / Panne, D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function.
Authors: Rengachari, S. / Groiss, S. / Devos, J.M. / Caron, E. / Grandvaux, N. / Panne, D.
History
DepositionJul 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon regulatory factor 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3382
Polymers21,2431
Non-polymers951
Water57632
1
A: Interferon regulatory factor 9
hetero molecules

A: Interferon regulatory factor 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6764
Polymers42,4862
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2170 Å2
ΔGint-26 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.770, 76.770, 85.605
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Interferon regulatory factor 9 / IRF-9 / IFN-alpha-responsive transcription factor subunit / ISGF3 p48 subunit / Interferon- ...IRF-9 / IFN-alpha-responsive transcription factor subunit / ISGF3 p48 subunit / Interferon-stimulated gene factor 3 gamma / ISGF-3 gamma / Transcriptional regulator ISGF3 subunit gamma


Mass: 21242.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irf9, Isgf3g / Production host: Escherichia coli (E. coli) / References: UniProt: Q61179
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 6.8, 1.5 M Ammonium phosphate monobasic and 0.1 M Ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.9→35.989 Å / Num. obs: 22803 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.923 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.041 / Χ2: 1.047 / Net I/σ(I): 14.81 / Num. measured all: 66645
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.012.3960.6561.4533140.8440.81588.3
2.01-2.153.0440.3773.1233950.9490.45696.8
2.15-2.323.1040.1795.9832740.9850.21598.8
2.32-2.542.9390.1019.2130050.9920.12398.8
2.54-2.843.1320.05815.7227450.9970.0799.4
2.84-3.283.0670.03824.6524300.9980.04598.9
3.28-4.012.8360.02633.7620610.9990.03298.2
4.01-5.643.0270.02240.3216180.9990.02797.9
5.64-35.9892.6880.02838.79610.9980.03496.6

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dsh

3dsh


Resolution: 1.9→35.989 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.39
RfactorNum. reflection% reflection
Rfree0.2421 1927 5.03 %
Rwork0.2069 --
obs0.2086 38295 85.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 297.71 Å2 / Biso mean: 76.8937 Å2 / Biso min: 32.89 Å2
Refinement stepCycle: final / Resolution: 1.9→35.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 5 32 1528
Biso mean--68.35 55.73 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141539
X-RAY DIFFRACTIONf_angle_d1.2632099
X-RAY DIFFRACTIONf_chiral_restr0.068226
X-RAY DIFFRACTIONf_plane_restr0.008280
X-RAY DIFFRACTIONf_dihedral_angle_d12.578930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.897-1.94450.3418930.37611815190860
1.9445-1.9970.34351170.33412191230871
1.997-2.05580.31051320.30552479261182
2.0558-2.12210.33051360.29252599273586
2.1221-2.1980.33131370.27572642277986
2.198-2.2860.32161440.25892625276988
2.286-2.390.29381390.25652679281888
2.39-2.5160.27761410.2522631277287
2.516-2.67360.26981430.24492692283588
2.6736-2.87990.28881430.22262789293292
2.8799-3.16960.24441480.22512796294493
3.1696-3.62780.24561440.20772768291291
3.6278-4.56920.21671540.16562813296793
4.5692-35.99570.19331560.17422849300593
Refinement TLS params.Method: refined / Origin x: 22.3049 Å / Origin y: 23.6272 Å / Origin z: 18.6301 Å
111213212223313233
T0.3054 Å20.041 Å2-0.0059 Å2-0.5231 Å20.0046 Å2--0.3016 Å2
L0.7357 °2-0.3581 °2-0.9006 °2-3.1148 °22.824 °2--5.2426 °2
S0.2634 Å °0.0553 Å °0.033 Å °-0.057 Å °-0.2498 Å °-0.0147 Å °-0.033 Å °-1.0026 Å °-0.0629 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA197 - 385
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 32

+
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