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- PDB-5bvi: X-ray Structure of Interferon Regulatory Factor 4 IAD Domain -

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Basic information

Entry
Database: PDB / ID: 5bvi
TitleX-ray Structure of Interferon Regulatory Factor 4 IAD Domain
ComponentsInterferon regulatory factor 4Interferon regulatory factors
KeywordsTRANSCRIPTION / Interferon Regulatory Factors / Transcription activation/Protein-DNA interaction
Function / homology
Function and homology information


nucleosome => GO:0000786 / : / : / negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production ...nucleosome => GO:0000786 / : / : / negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of DNA binding / positive regulation of interleukin-2 production / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA 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 / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Tumour Suppressor Smad4 - #10 / 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 / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain ...Tumour Suppressor Smad4 - #10 / 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 / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interferon regulatory factor 4 / Interferon regulatory factor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEscalate, C.R. / Remesh, S.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM092854 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21-CA179008 United States
Virginia Commonwealth UniversityVCU-PRQF AWARD United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Studies of IRF4 Reveal a Flexible Autoinhibitory Region and a Compact Linker Domain.
Authors: Remesh, S.G. / Santosh, V. / Escalante, C.R.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon regulatory factor 4
B: Interferon regulatory factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0696
Polymers42,9272
Non-polymers1424
Water2,072115
1
A: Interferon regulatory factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5704
Polymers21,4631
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon regulatory factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4992
Polymers21,4631
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.533, 84.854, 149.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
DetailsMonomer confirmed by analytical ultracentrifugation

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Components

#1: Protein Interferon regulatory factor 4 / Interferon regulatory factors / Interferon regulatory factor 4 / isoform CRA_b


Mass: 21463.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irf4, mCG_4922 / Plasmid: pet15TEV_NESG
Details (production host): EvNO00338203 (pet15b with TEV site)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS star / References: UniProt: Q5SUZ4, UniProt: Q64287*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 1.5-1.7M KCl, 0.1M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 23107 / % possible obs: 93.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.7
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSH

3dsh


Resolution: 2.6→32.337 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 1531 8.94 %
Rwork0.1937 --
obs0.1991 17124 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→32.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 4 115 3027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092981
X-RAY DIFFRACTIONf_angle_d1.1454048
X-RAY DIFFRACTIONf_dihedral_angle_d14.5921106
X-RAY DIFFRACTIONf_chiral_restr0.042439
X-RAY DIFFRACTIONf_plane_restr0.006532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68390.32561360.2391394X-RAY DIFFRACTION92
2.6839-2.77980.31751380.2331402X-RAY DIFFRACTION94
2.7798-2.8910.3231370.22571399X-RAY DIFFRACTION93
2.891-3.02250.31441410.22061433X-RAY DIFFRACTION93
3.0225-3.18170.29591380.21971398X-RAY DIFFRACTION93
3.1817-3.38080.27381380.20571400X-RAY DIFFRACTION92
3.3808-3.64160.23381380.17751417X-RAY DIFFRACTION93
3.6416-4.00740.25041410.17591428X-RAY DIFFRACTION93
4.0074-4.58590.19371390.1581429X-RAY DIFFRACTION92
4.5859-5.77240.21621410.17111432X-RAY DIFFRACTION91
5.7724-32.33910.23771440.20021461X-RAY DIFFRACTION88

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