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- PDB-3dsh: Crystal structure of dimeric interferon regulatory factor 5 (IRF-... -

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Basic information

Entry
Database: PDB / ID: 3dsh
TitleCrystal structure of dimeric interferon regulatory factor 5 (IRF-5) transactivation domain
ComponentsInterferon regulatory factor 5Interferon regulatory factors
KeywordsDNA BINDING PROTEIN / Phosphoactivation induced dimerization / DNA-binding / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


response to peptidoglycan / chromatin => GO:0000785 / immune system process / type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / response to muramyl dipeptide / type II interferon-mediated signaling pathway / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / Interferon gamma signaling ...response to peptidoglycan / chromatin => GO:0000785 / immune system process / type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / response to muramyl dipeptide / type II interferon-mediated signaling pathway / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / Interferon gamma signaling / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / 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 / positive regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Interferon regulatory factor 5 / 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 5 / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsChen, W. / Lam, S.S. / Srinath, H. / Jiang, Z. / Correia, J.J. / Schiffer, C. / Fitzgerald, K.A. / Lin, K. / Royer Jr., W.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5.
Authors: Chen, W. / Lam, S.S. / Srinath, H. / Jiang, Z. / Correia, J.J. / Schiffer, C.A. / Fitzgerald, K.A. / Lin, K. / Royer, W.E.
History
DepositionJul 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon regulatory factor 5


Theoretical massNumber of molelcules
Total (without water)28,5961
Polymers28,5961
Non-polymers00
Water2,378132
1
A: Interferon regulatory factor 5

A: Interferon regulatory factor 5


Theoretical massNumber of molelcules
Total (without water)57,1922
Polymers57,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5890 Å2
ΔGint-21 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.162, 66.162, 156.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Interferon regulatory factor 5 / Interferon regulatory factors / IRF-5


Mass: 28595.842 Da / Num. of mol.: 1
Fragment: IRF-5 transactivation domain (UNP residues 232-477)
Mutation: S430D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF5 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q13568
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5-2.0% PEG 6000, 100mM imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X29A11.1
ROTATING ANODERIGAKU RUH3R21.54178
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 1, 2007
RIGAKU RAXIS IV2IMAGE PLATEJan 1, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.541781
ReflectionResolution: 2→100 Å / Num. all: 26875 / Num. obs: 26875 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.0229 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2→30.46 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.285 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24241 1342 5 %RANDOM
Rwork0.20448 ---
all0.206 25440 --
obs0.20632 25440 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 0 132 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221988
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9782699
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6724.24299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1715350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.7061514
X-RAY DIFFRACTIONr_chiral_restr0.1220.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021531
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.3806
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.51348
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.5197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.352
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.540
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.19221217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.24231944
X-RAY DIFFRACTIONr_scbond_it2.5372855
X-RAY DIFFRACTIONr_scangle_it3.7873755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 67 -
Rwork0.207 1468 -
obs--77.14 %
Refinement TLS params.Method: refined / Origin x: 11.439 Å / Origin y: 35.825 Å / Origin z: 72.601 Å
111213212223313233
T-0.1297 Å20.0525 Å20.014 Å2-0.1016 Å2-0.0496 Å2---0.1536 Å2
L0.3686 °2-0.104 °20.0891 °2-0.4578 °20.0792 °2--3.3275 °2
S-0.1189 Å °0.2197 Å °-0.0571 Å °0.1509 Å °0.0332 Å °0.0673 Å °-0.2464 Å °-0.243 Å °0.0858 Å °

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