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- PDB-3ub3: D96N variant of TIR domain of Mal/TIRAP -

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Basic information

Entry
Database: PDB / ID: 3ub3
TitleD96N variant of TIR domain of Mal/TIRAP
ComponentsToll/interleukin-1 receptor domain-containing adapter protein
KeywordsIMMUNE SYSTEM / TIR domain / TLRs adaptor
Function / homology
Function and homology information


positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / myeloid cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / regulation of stress-activated MAPK cascade / regulation of innate immune response / cellular response to lipoteichoic acid / endocytic vesicle / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of B cell proliferation / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-12 production / positive regulation of interleukin-8 production / protein kinase C binding / positive regulation of JNK cascade / positive regulation of protein-containing complex assembly / ruffle membrane / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / molecular adaptor activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / innate immune response / cell surface / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Toll-interleukin 1 receptor domain-containing adaptor protein, Tirap / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Toll/interleukin-1 receptor domain-containing adapter protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsShen, Y. / Lin, Z.
CitationJournal: Plos One / Year: 2012
Title: Structural Insights into TIR Domain Specificity of the Bridging Adaptor Mal in TLR4 Signaling
Authors: Lin, Z. / Lu, J. / Zhou, W. / Shen, Y.
History
DepositionOct 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll/interleukin-1 receptor domain-containing adapter protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1232
Polymers15,9691
Non-polymers1541
Water362
1
A: Toll/interleukin-1 receptor domain-containing adapter protein
hetero molecules

A: Toll/interleukin-1 receptor domain-containing adapter protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2474
Polymers31,9382
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2150 Å2
ΔGint-23 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.916, 86.916, 81.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Toll/interleukin-1 receptor domain-containing adapter protein / MAL / TIR domain-containing adapter protein / Adaptor protein Wyatt / MyD88 adapter-like protein


Mass: 15969.173 Da / Num. of mol.: 1 / Fragment: TIR domain, UNP residues 78-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIRAP, MAL / Production host: Escherichia coli (E. coli) / References: UniProt: P58753
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 7 AND 12 OF DATABASE UNIPROTKB/SWISS-PROT P58753 (TIRAP_HUMAN). ...THE SEQUENCE IS BASED ON REFERENCE 7 AND 12 OF DATABASE UNIPROTKB/SWISS-PROT P58753 (TIRAP_HUMAN). RESIDUE D96N IS A NATURAL VARIANT.

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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: 4.8 Å3/Da / Density % sol: 74.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 12-15% Glycerol, 0.2-0.3M sodium chloride, 10mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 8535 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 78.1 Å2
Reflection shellResolution: 2.75→2.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UB2

3ub2


Resolution: 2.75→38.87 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 873382.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 442 5.2 %RANDOM
Rwork0.245 ---
all0.245 8535 --
obs0.245 8489 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4178 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 70.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.58 Å20 Å20 Å2
2---7.58 Å20 Å2
3---15.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.75→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 8 2 981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 71 5.2 %
Rwork0.326 1284 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6dtt.paramdtt.top

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