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- PDB-4bsx: Crystal Structure of the N terminal domain of TRIF (TIR-domain- c... -

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Basic information

Entry
Database: PDB / ID: 4bsx
TitleCrystal Structure of the N terminal domain of TRIF (TIR-domain- containing adapter-inducing interferon-beta)
ComponentsTIR DOMAIN-CONTAINING ADAPTER MOLECULE 1
KeywordsAPOPTOSIS / INNATE IMMUNITY / TETRATRICO-PEPTIDE REPEAT (TPR) / IFIT PROTEINS
Function / homology
Function and homology information


TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / positive regulation of natural killer cell activation / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of myeloid dendritic cell cytokine production ...TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / positive regulation of natural killer cell activation / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of myeloid dendritic cell cytokine production / Caspase activation via Death Receptors in the presence of ligand / toll-like receptor 3 signaling pathway / TRIF-dependent toll-like receptor signaling pathway / RIP-mediated NFkB activation via ZBP1 / macrophage activation involved in immune response / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / response to exogenous dsRNA / B cell proliferation / regulation of protein-containing complex assembly / autophagosome / positive regulation of type I interferon production / positive regulation of autophagy / signaling adaptor activity / positive regulation of chemokine production / positive regulation of B cell proliferation / lipopolysaccharide-mediated signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / nitric oxide biosynthetic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interferon-beta production / TICAM1, RIP1-mediated IKK complex recruitment / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / apoptotic signaling pathway / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / molecular adaptor activity / early endosome / endosome membrane / endosome / inflammatory response / innate immune response / positive regulation of gene expression / protein kinase binding / mitochondrion / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #780 / TIR domain-containing adapter molecule 1 / TRIF, N-terminal / : / TRIF N-terminal domain / RHIM domain / RIP homotypic interaction motif / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #780 / TIR domain-containing adapter molecule 1 / TRIF, N-terminal / : / TRIF N-terminal domain / RHIM domain / RIP homotypic interaction motif / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
TIR domain-containing adapter molecule 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.229 Å
AuthorsUllah, M.O. / Ve, T. / Mangan, M. / Alaidarous, M. / Sweet, M.J. / Mansell, A. / Kobe, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The Tlr Signalling Adaptor Trif/Ticam-1 Has an N-Terminal Helical Domain with Structural Similarity to Ifit Proteins
Authors: Ullah, M.O. / Ve, T. / Mangan, M. / Alaidarous, M. / Sweet, M.J. / Mansell, A. / Kobe, B.
History
DepositionJun 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1
B: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1
C: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1
D: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)69,1484
Polymers69,1484
Non-polymers00
Water5,206289
1
A: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,2871
Polymers17,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,2871
Polymers17,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,2871
Polymers17,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,2871
Polymers17,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.307, 49.331, 70.142
Angle α, β, γ (deg.)88.66, 77.63, 72.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 5:147 ) AND (NOT ELEMENT H)
211CHAIN B AND (RESSEQ 5:147 ) AND (NOT ELEMENT H)
311CHAIN C AND (RESSEQ 5:147 ) AND (NOT ELEMENT H)
411CHAIN D AND (RESSEQ 5:147 ) AND (NOT ELEMENT H)

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Components

#1: Protein
TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1 / TICAM-1 / PROLINE-RICH / VINCULIN AND TIR DOMAIN-CONTAINING PROTEIN B / PUTATIVE NF-KAPPA-B- ...TICAM-1 / PROLINE-RICH / VINCULIN AND TIR DOMAIN-CONTAINING PROTEIN B / PUTATIVE NF-KAPPA-B-ACTIVATING PROTEIN 502H / TOLL-INTERLEUKIN-1 RECEPTOR DOMAIN-CONTAINING ADAPTER PROTEIN INDUCING INTERFERON BETA / MYD88-3 / TIR DOMAIN-CONTAINING ADAPTER PROTEIN INDUCING IFN-BETA / TRIF


Mass: 17286.967 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-153 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IUC6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 0.1M BIS-TRIS PH 6.6, 150MM NACL, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.1070, 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1071
20.97931
ReflectionResolution: 2.22→68.44 Å / Num. obs: 27104 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 3.83 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.72
Reflection shellResolution: 2.22→2.35 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 71.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.229→47.084 Å / SU ML: 0.24 / σ(F): 0.02 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 1877 7.3 %
Rwork0.1906 --
obs0.1942 25722 88.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.229→47.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 0 289 4776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144571
X-RAY DIFFRACTIONf_angle_d1.3586191
X-RAY DIFFRACTIONf_dihedral_angle_d14.5171739
X-RAY DIFFRACTIONf_chiral_restr0.067684
X-RAY DIFFRACTIONf_plane_restr0.006816
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1114X-RAY DIFFRACTIONPOSITIONAL
12B1114X-RAY DIFFRACTIONPOSITIONAL0.062
13C1114X-RAY DIFFRACTIONPOSITIONAL0.057
14D1114X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2293-2.28950.3107750.233988X-RAY DIFFRACTION48
2.2895-2.35690.28491270.21441671X-RAY DIFFRACTION80
2.3569-2.4330.28111490.2091807X-RAY DIFFRACTION89
2.433-2.51990.28541430.20911821X-RAY DIFFRACTION89
2.5199-2.62080.29541510.19481907X-RAY DIFFRACTION91
2.6208-2.74010.24221440.20191834X-RAY DIFFRACTION90
2.7401-2.88450.24551510.1931933X-RAY DIFFRACTION93
2.8845-3.06520.28421500.19741926X-RAY DIFFRACTION94
3.0652-3.30180.2341570.20041975X-RAY DIFFRACTION96
3.3018-3.6340.1961560.17711958X-RAY DIFFRACTION95
3.634-4.15960.21951550.16311976X-RAY DIFFRACTION96
4.1596-5.23950.20581600.16762026X-RAY DIFFRACTION98
5.2395-47.09440.22271590.20732023X-RAY DIFFRACTION98

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