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- PDB-2y92: Crystal structure of MAL adaptor protein -

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Basic information

Entry
Database: PDB / ID: 2y92
TitleCrystal structure of MAL adaptor protein
ComponentsTOLL/INTERLEUKIN-1 RECEPTOR DOMAIN-CONTAINING ADAPTER PROTEIN,
KeywordsIMMUNE SYSTEM / TOLL-LIKE RECEPTOR SIGNALING / INNATE IMMUNITY
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: 3.01 Å
AuthorsValkov, E. / Stamp, A. / Martin, J.L. / Kobe, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal Structure of Toll-Like Receptor Adaptor Mal/Tirap Reveals the Molecular Basis for Signal Transduction and Disease Protection.
Authors: Valkov, E. / Stamp, A. / Dimaio, F. / Baker, D. / Verstak, B. / Roversi, P. / Kellie, S. / Sweet, M.J. / Mansell, A. / Gay, N.J. / Martin, J.L. / Kobe, B.
History
DepositionFeb 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)16,0672
Polymers15,9131
Non-polymers1541
Water00
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)32,1354
Polymers31,8262
Non-polymers3092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2190 Å2
ΔGint-24.1 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.146, 88.146, 78.793
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, / TIR DOMAIN-CONTAINING ADAPTER PROTEIN / ADAPTOR PROTEIN WYATT / MYD88 ADAPTER-LIKE PROTEIN / MAL


Mass: 15913.106 Da / Num. of mol.: 1 / Fragment: TIR DOMAIN, RESIDUES 79-221
Source method: isolated from a genetically manipulated source
Details: C91 AND C157 MODIFIED BY DITHIOTHREITOL (DTT) / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.81 Å3/Da / Density % sol: 77 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0722
DetectorType: ADSC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 6390 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Biso Wilson estimate: 112.82 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.5
Reflection shellResolution: 3.01→3.37 Å / Mean I/σ(I) obs: 2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z5V

2z5v


Resolution: 3.01→48.88 Å / Cor.coef. Fo:Fc: 0.9201 / Cor.coef. Fo:Fc free: 0.8969 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 306 4.79 %RANDOM
Rwork0.23 ---
obs0.231 6390 --
Displacement parametersBiso mean: 94.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.9298 Å20 Å20 Å2
2--0.9298 Å20 Å2
3----1.8596 Å2
Refine analyzeLuzzati coordinate error obs: 0.753 Å
Refinement stepCycle: LAST / Resolution: 3.01→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 8 0 989
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071012HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.891371HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d345SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes22HARMONIC2
X-RAY DIFFRACTIONt_gen_planes145HARMONIC5
X-RAY DIFFRACTIONt_it1005HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.56
X-RAY DIFFRACTIONt_other_torsion19.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion126SEMIHARMONIC5
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_contact1050SEMIHARMONIC4
LS refinement shellResolution: 3.01→3.37 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2857 80 4.6 %
Rwork0.2712 1661 -
all0.2718 1741 -
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)
111.885-3.86770.411110.12443.2658.1053-0.0241-0.18320.12230.12770.08540.0859-0.2805-0.1634-0.0613-0.06740.0077-0.0255-0.159-0.0495-0.1965-14.030935.7406-5.5216
20-0.29112.17630.17951.94970.3409-0.0158-0.0887-0.28720.0051-0.0317-0.15810.17720.07010.0474-0.05220.00070.0457-0.21050.0982-0.0398-10.443321.9789-11.2419
34.54475.8116-2.54694.79345.33161.9491-0.03950.08560.0552-0.1347-0.01710.2516-0.0455-0.14480.05660.0627-0.24050.0993-0.10150.01990.0124-18.235724.2582-14.3409
46.2769-1.1967-0.6560.06572.88227.4493-0.05260.06760.1264-0.0260.30320.05-0.35810.0513-0.2506-0.0341-0.14420.1384-0.12310.06840.0853-7.889831.4151-18.6201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A79 - A142 )
2X-RAY DIFFRACTION2(A143 - A153 )
3X-RAY DIFFRACTION3(A154 - A179 )
4X-RAY DIFFRACTION4(A180 - A220 )

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