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- PDB-4c0m: Crystal Structure of the N terminal domain of wild type TRIF (TIR... -

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Basic information

Entry
Database: PDB / ID: 4c0m
TitleCrystal Structure of the N terminal domain of wild type TRIF (TIR- domain-containing adapter-inducing interferon-beta)
ComponentsTIR DOMAIN-CONTAINING ADAPTER MOLECULE 1
KeywordsIMMUNE SYSTEM / TOLL-LIKE RECEPTOR ADAPTOR PROTEIN / INNATE IMMUNITY / TETRATRICO-PEPTIDE REPEAT (TPR) / IFIT PROTEINS
Function / homology
Function and homology information


TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / positive regulation of myeloid dendritic cell cytokine production / cellular response to oxidised low-density lipoprotein particle stimulus / Caspase activation via Death Receptors in the presence of ligand ...TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / positive regulation of myeloid dendritic cell cytokine production / cellular response to oxidised low-density lipoprotein particle stimulus / 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 natural killer cell activation / 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 / signaling adaptor activity / positive regulation of autophagy / positive regulation of B cell proliferation / positive regulation of chemokine production / 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 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / nitric oxide biosynthetic process / 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 nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionAug 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)68,0854
Polymers68,0854
Non-polymers00
Water0
1
A: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,0211
Polymers17,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,0211
Polymers17,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,0211
Polymers17,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)17,0211
Polymers17,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.000, 49.400, 70.910
Angle α, β, γ (deg.)88.56, 77.20, 72.11
Int Tables number1
Space group name H-MP1

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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: 17021.229 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-153
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) / Variant (production host): B834 / References: UniProt: Q8IUC6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growDetails: 0.1 M BIS TRIS PH 6.6, 150 MM NACL AND 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.8→44.51 Å / Num. obs: 13337 / % possible obs: 89.6 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 34.21 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 90.4

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BSX

4bsx


Resolution: 2.8→39.7 Å / Cor.coef. Fo:Fc: 0.8277 / Cor.coef. Fo:Fc free: 0.7729 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.458
RfactorNum. reflection% reflectionSelection details
Rfree0.2912 680 5.1 %RANDOM
Rwork0.2516 ---
obs0.2537 13335 89.58 %-
Displacement parametersBiso mean: 22.66 Å2
Baniso -1Baniso -2Baniso -3
1-14.6405 Å2-2.5178 Å20.4198 Å2
2---13.8142 Å2-6.5178 Å2
3----0.8264 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 0 0 4352
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014428HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975999HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2107SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes643HARMONIC5
X-RAY DIFFRACTIONt_it4428HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion2.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion552SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4769SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.02 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2318 137 4.91 %
Rwork0.2505 2654 -
all0.2496 2791 -
obs--89.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6748-0.15190.14850.0347-2.133-0.31610.0117-0.01020.0132-0.0238-0.0156-0.02690.0153-0.0220.0039-0.1158-0.02120.01810.06890.16860.00029.194152.991849.7823
22.0378-0.38570.480.2239-1.36511.15930.00340.00720.0353-0.0032-0.0296-0.0038-0.0259-0.02620.0262-0.1162-0.0448-0.0030.09410.1157-0.028744.239934.366417.5179
31.92-0.0827-0.2081-0.2332-1.72931.2866-0.00220.0303-0.006-0.0065-0.0035-0.00770.02690.01880.0056-0.1438-0.03290.0090.09750.1087-0.038420.371517.52734.1388
42.2949-0.17650.01680.184-1.89290.41460.0146-0.00430.00220.0439-0.0186-0.04720.01370.01030.004-0.0811-0.02920.01210.07890.0768-0.057417.682245.80611.9037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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