[English] 日本語
Yorodumi
- PDB-1if1: INTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1if1
TitleINTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA
Components
  • DNA (26-MER)
  • PROTEIN (INTERFERON REGULATORY FACTOR 1)
KeywordsTRANSCRIPTION/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / TRANSCRIPTION FACTOR / INTERFERON REGULATION / HELIX-TURN-HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


CD8-positive, alpha-beta T cell differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / regulation of cell cycle => GO:0051726 / positive regulation of natural killer cell differentiation / : / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of adaptive immune response / positive regulation of T-helper 1 cell differentiation / negative regulation of regulatory T cell differentiation / negative regulation of T-helper 2 cell differentiation ...CD8-positive, alpha-beta T cell differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / regulation of cell cycle => GO:0051726 / positive regulation of natural killer cell differentiation / : / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of adaptive immune response / positive regulation of T-helper 1 cell differentiation / negative regulation of regulatory T cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of tyrosine phosphorylation of STAT protein / chromatin => GO:0000785 / response to growth hormone / cellular response to peptide hormone stimulus / regulation of innate immune response / immune system process / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / cellular response to interferon-beta / cellular response to interleukin-1 / type II interferon-mediated signaling pathway / positive regulation of interferon-beta production / positive regulation of interleukin-12 production / cellular response to mechanical stimulus / cellular response to tumor necrosis factor / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Interferon regulatory factor 1 / Interferon regulatory factor-1/2 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Interferon regulatory factor 1 / Interferon regulatory factor-1/2 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon regulatory factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsEscalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.
Citation
Journal: Nature / Year: 1998
Title: Structure of IRF-1 with bound DNA reveals determinants of interferon regulation.
Authors: Escalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.K.
#1: Journal: FEBS Lett. / Year: 1997
Title: Expression, Purification, and Co-Crystallization of Irf-1 Bound to the Interferon-Beta Element Prdi
Authors: Escalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.K.
History
DepositionSep 12, 1997Processing site: NDB
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (26-MER)
D: DNA (26-MER)
A: PROTEIN (INTERFERON REGULATORY FACTOR 1)
B: PROTEIN (INTERFERON REGULATORY FACTOR 1)


Theoretical massNumber of molelcules
Total (without water)42,8124
Polymers42,8124
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.800, 84.800, 203.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.823802, 0.55224, -0.127987), (0.566506, 0.79384, -0.221107), (-0.020503, -0.254654, -0.966815)
Vector: 106.722, -28.833, 29.2859)

-
Components

#1: DNA chain DNA (26-MER)


Mass: 7986.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein PROTEIN (INTERFERON REGULATORY FACTOR 1)


Mass: 13419.605 Da / Num. of mol.: 2 / Fragment: DNA-BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: MOUSE FIBROBLAST L929 / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P15314
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 18-22% PEG8K, 300 MM AMMONIUM ACETATE (PH 6.5), 10% GLYCEROL.
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: Escalante, C.R., (1997) FEBS Lett., 414, 219.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 %PEG800011
2300 mMammonium acetate11

-
Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 1, 1996 / Details: DUAL SLITS
RadiationMonochromator: SILICON CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 20328 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 15.3
Reflection shellResolution: 3→3.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 13.5 / Rsym value: 0.09 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 21657 / % possible obs: 99.1 % / Num. measured all: 125805
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.23 Å / % possible obs: 99.7 %

-
Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3→12 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.309 -10 %RANDOM
Rwork0.242 ---
obs0.242 20328 --
Displacement parametersBiso mean: 29.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.642 Å20 Å2
2--0.642 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 1054 0 10 2779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINTS30.066300300
2230.08300300
3350.0741010
4450.0591010
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMODDNA-RNA.TOPMOD
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.97 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg2.3

+
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