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- PDB-9hgh: MyD88 peptide_1 bound to SPOP MATH domain -

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Basic information

Entry
Database: PDB / ID: 9hgh
TitleMyD88 peptide_1 bound to SPOP MATH domain
Components
  • Myeloid differentiation primary response protein MyD88
  • Speckle type BTB/POZ protein
KeywordsLIGASE / Ubiquitination / Immune signalling / Degradation
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response ...regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / response to molecule of fungal origin / positive regulation of lymphocyte proliferation / response to peptidoglycan / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / regulation of neutrophil migration / IRAK4 deficiency (TLR5) / establishment of endothelial intestinal barrier / MyD88 dependent cascade initiated on endosome / cellular response to oxidised low-density lipoprotein particle stimulus / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / Toll-like receptor binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / toll-like receptor TLR6:TLR2 signaling pathway / interleukin-33-mediated signaling pathway / neutrophil activation involved in immune response / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / interleukin-1 receptor binding / death receptor binding / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / extrinsic component of cytoplasmic side of plasma membrane / interleukin-1-mediated signaling pathway / extrinsic component of plasma membrane / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / skin development / defense response to protozoan / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-17 production / response to amine / immunoglobulin mediated immune response / response to amino acid / positive regulation of type I interferon production / phagocytosis / positive regulation of chemokine production / JNK cascade / signaling adaptor activity / response to interleukin-1 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / protein catabolic process / positive regulation of interleukin-6 production / Interleukin-1 signaling / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / ER-Phagosome pathway / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / gene expression / molecular adaptor activity / defense response to virus / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / endosome membrane / defense response to bacterium / innate immune response / apoptotic process / positive regulation of gene expression / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myeloid differentiation primary response protein MyD88 / MyD88, death domain / MATH domain / MATH/TRAF domain / TIR domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / MATH domain / MATH/TRAF domain / TIR domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / BTB/POZ domain / BTB domain profile. / BTB/POZ domain / Death-like domain superfamily / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Speckle type BTB/POZ protein / Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMakhlouf, L. / Zeqiraj, E.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome Trust222372/Z/21/Z United Kingdom
Wellcome Trust222531/Z/21/Z United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01HL159175-04 United States
CitationJournal: Biochem.J. / Year: 2025
Title: Sequence rules for a long SPOP-binding degron required for protein ubiquitylation.
Authors: Makhlouf, L. / Mishra, M. / Makhlouf, H. / Manfield, I. / Busino, L. / Zeqiraj, E.
History
DepositionNov 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle type BTB/POZ protein
B: Myeloid differentiation primary response protein MyD88


Theoretical massNumber of molelcules
Total (without water)17,9832
Polymers17,9832
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-5 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 57.290, 60.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Speckle type BTB/POZ protein


Mass: 16212.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: D6RDG8
#2: Protein/peptide Myeloid differentiation primary response protein MyD88


Mass: 1769.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99836
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.9→33.44 Å / Num. obs: 11453 / % possible obs: 99.4 % / Redundancy: 5.8 % / CC1/2: 0.99 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 1091 / CC1/2: 0.76 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.44 Å / SU ML: 0.1939 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2322 547 4.78 %
Rwork0.173 10904 -
obs0.1758 11451 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 121 1340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111243
X-RAY DIFFRACTIONf_angle_d1.13211670
X-RAY DIFFRACTIONf_chiral_restr0.0606184
X-RAY DIFFRACTIONf_plane_restr0.0101209
X-RAY DIFFRACTIONf_dihedral_angle_d6.1476163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.27221330.19492639X-RAY DIFFRACTION98.54
2.09-2.390.25081230.17082709X-RAY DIFFRACTION99.96
2.39-3.020.23861530.18072707X-RAY DIFFRACTION99.62
3.02-33.440.21021380.16392849X-RAY DIFFRACTION99.37
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)
16.214269863950.0277075364085-1.316403316781.526406281610.4904590745341.89354448155-0.2690044369410.3632728837310.4695061247750.1008801872140.228952638809-0.05148475338380.04801102684380.09944390885330.02936843075730.07956851841080.0136914890506-0.01122460755810.1175247224650.01680446775330.118807193795.20117689989.136907603530.6371275507
22.10206261405-2.06791016241-0.1961359439552.919411502161.266392924012.10026680384-0.04096338960830.244696496681-0.469703728101-0.1030866128070.1130009917650.1072316104710.5709388021250.047770445980.1326149599730.1760059023680.0122476810731-0.04584025225890.227885687365-0.03801999173580.255593575364-16.5884238803-1.095127030063.00553711857
32.7029619391-0.0548230082151-0.9904534215652.232835914890.04521128539232.936390462070.03855256298360.183931311710.351042209178-0.2319631872620.09176878096780.0991266653229-0.0614542965998-0.0701028874127-0.04865134141760.1119642577210.0159621059465-0.00642257719270.1095484561240.01172821263830.09992666989871.179890176214.14099970878-5.51362552302
42.042523901220.63854072678-0.02925617460034.919862453481.392014595533.73338057637-0.06475175949380.0994983031264-0.2970874003060.311495937916-0.008768165147740.3913604995680.629921875404-0.042533396460.04905609362990.230560277702-0.04465841684680.04658300246790.190127733103-0.01480438636620.180271790795-8.12176118569-10.32059563647.75332612202
52.59007878434-0.385248100061-1.854758408071.25604132060.1797211900374.121959264310.1164424018520.094256154533-0.0473703645995-0.2441770625590.0536785271904-0.135478185730.2286442267620.154714047525-0.0515574054090.101371242682-0.01836530658680.000111827614150.125917288084-0.01541190805880.11395658176.11187769355-1.07895950133-6.44921041932
64.38472058474-0.97767400846-2.827530054351.349416077811.056309525573.37201983349-0.0370590650287-0.3217105925040.1816413177920.07284656344670.161228468423-0.1998839502490.2223178912530.406469062687-0.1658893712790.1267713034370.0135605050113-0.008415488241480.1057934717440.01136518531730.09443176002418.095988690992.212795534244.05947141297
74.37843526978-3.111311953251.033996603816.110758733810.07277208919441.47345989763-0.23934326052-0.3796478211960.846879112550.410799785586-0.04602327947930.0973508164074-0.290107401592-0.1643666045620.03949207758620.2051211825130.0424644998811-0.04171077909920.197987988583-0.07876373695520.223658525607-2.434884658319.8296295549615.0164678561
81.664948104760.0350900923273-0.3772650942231.5635602705-0.01875979634112.40582148953-0.00193777173151-0.168961179656-0.1310450641240.06974547822140.0333578427293-0.06431723574390.2424065380460.2294864995280.009514655818920.09211992423170.01184907349920.004075840531760.06843860605770.01642822520920.100886399115.79032799764-4.312105847533.51385359157
92.890965551041.173541112220.5592919257235.220782678433.394965755226.767903833090.0668363624877-0.120733396956-0.3179347065080.1514569125770.01066798614390.6417792118350.0151370383363-0.4324853441150.08889376243430.295522369274-0.03160952436560.01830821155240.283684024284-0.01646126233780.197662113805-11.77916284330.69773204572216.8151896056
104.20089125958-0.334496099048-1.390993879391.367518910380.6211554031351.82454416770.144401503902-0.1099482434820.4701499611460.0410954569635-0.02209781883690.0598365029598-0.0919052746392-0.07034172260810.01208392099730.12428117322-0.0213070993136-0.01069076855710.08460085532810.009358135521270.0999447317496-2.052211846077.548311085856.20749419941
112.56523560445-0.282914126298-0.3689347283882.014881250020.3514412504961.50734106558-0.165827925062-0.0961900767043-0.3087424744120.001328962073890.1075798242570.003508722344010.561038286779-0.594051101750.02033687916530.241364690906-0.0605791302519-0.04154857991440.1871948477990.01352624410280.1453790248990.164256008463-9.285000021689.16195504139
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 38 )AA27 - 381 - 12
22chain 'A' and (resid 39 through 48 )AA39 - 4813 - 22
33chain 'A' and (resid 49 through 72 )AA49 - 7223 - 46
44chain 'A' and (resid 73 through 84 )AA73 - 8447 - 58
55chain 'A' and (resid 85 through 97 )AA85 - 9759 - 71
66chain 'A' and (resid 98 through 106 )AA98 - 10672 - 80
77chain 'A' and (resid 107 through 116 )AA107 - 11681 - 90
88chain 'A' and (resid 117 through 138 )AA117 - 13891 - 112
99chain 'A' and (resid 139 through 147 )AA139 - 147113 - 121
1010chain 'A' and (resid 148 through 165 )AA148 - 165122 - 139
1111chain 'B' and (resid 126 through 140 )BB126 - 1401 - 15

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