[English] 日本語
Yorodumi
- PDB-8jks: T95R mutant IRF4 DNA-binding domain bound to an DNA containing GA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jks
TitleT95R mutant IRF4 DNA-binding domain bound to an DNA containing GAGA motif
Components
  • GAGA-Forward
  • GAGA-Reverse
  • Interferon regulatory factor 4
KeywordsTRANSCRIPTION / IRF4 / transcription factor / protein-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / 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
DNA / DNA (> 10) / Interferon regulatory factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang, G. / Feng, X. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Structure / Year: 2023
Title: Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency.
Authors: Wang, G. / Feng, X. / Ding, J.
History
DepositionJun 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GAGA-Forward
B: GAGA-Reverse
C: Interferon regulatory factor 4
D: Interferon regulatory factor 4
E: GAGA-Forward
F: GAGA-Reverse
G: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)77,8878
Polymers77,8878
Non-polymers00
Water00
1
A: GAGA-Forward
B: GAGA-Reverse
C: Interferon regulatory factor 4
D: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)38,9444
Polymers38,9444
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-44 kcal/mol
Surface area17600 Å2
MethodPISA
2
E: GAGA-Forward
F: GAGA-Reverse
G: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)38,9444
Polymers38,9444
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-48 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.610, 68.010, 246.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain GAGA-Forward


Mass: 5816.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain GAGA-Reverse


Mass: 5833.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Interferon regulatory factor 4 / Interferon regulatory factor 4 / isoform CRA_e


Mass: 13646.490 Da / Num. of mol.: 4 / Fragment: DNA-binding domain / Mutation: T95R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, hCG_20902 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z3D5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.0) and 10% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9752 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9752 Å / Relative weight: 1
ReflectionResolution: 3.3→41.03 Å / Num. obs: 13978 / % possible obs: 99.7 % / Redundancy: 12.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.072 / Rrim(I) all: 0.262 / Χ2: 1.01 / Net I/σ(I): 10.1 / Num. measured all: 180176
Reflection shellResolution: 3.3→3.39 Å / % possible obs: 99.1 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.382 / Num. measured all: 13384 / Num. unique obs: 981 / CC1/2: 0.993 / Rpim(I) all: 0.388 / Rrim(I) all: 1.437 / Χ2: 0.94 / Net I/σ(I) obs: 2.8

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8JKL

8jkl


Resolution: 3.3→40.02 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 693 5.02 %
Rwork0.235 --
obs0.2376 13818 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 1560 0 0 5218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035508
X-RAY DIFFRACTIONf_angle_d0.9877764
X-RAY DIFFRACTIONf_dihedral_angle_d26.3021231
X-RAY DIFFRACTIONf_chiral_restr0.072799
X-RAY DIFFRACTIONf_plane_restr0.006735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.550.35251450.32282471X-RAY DIFFRACTION96
3.55-3.910.35591420.26252580X-RAY DIFFRACTION99
3.91-4.480.26961120.2412645X-RAY DIFFRACTION100
4.48-5.640.24741430.24622662X-RAY DIFFRACTION100
5.64-40.020.27511510.19952767X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.3457 Å / Origin y: 14.8786 Å / Origin z: -29.0331 Å
111213212223313233
T0.6911 Å20.0364 Å2-0.0366 Å2-0.7356 Å2-0.1043 Å2--0.6512 Å2
L0.9073 °20.4009 °2-0.0949 °2-0.8491 °2-0.2599 °2---0.1486 °2
S0.1112 Å °0.2065 Å °-0.0678 Å °0.2608 Å °-0.0937 Å °-0.0579 Å °-0.1221 Å °0.0105 Å °-0 Å °
Refinement TLS groupSelection details: all

+
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