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- PDB-9hfv: MyD88 peptide_2 bound to SPOP MATH domain -

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Basic information

Entry
Database: PDB / ID: 9hfv
TitleMyD88 peptide_2 bound to SPOP MATH domain
Components
  • Myeloid differentiation primary response protein MyD88
  • Speckle-type 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 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / cellular response to oxidised low-density lipoprotein particle stimulus / 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 / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / death receptor binding / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / extrinsic component of cytoplasmic side of plasma membrane / MyD88-dependent toll-like receptor signaling pathway / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / skin development / type I interferon-mediated signaling pathway / response to amine / defense response to protozoan / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of type I interferon production / phagocytosis / response to amino acid / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of chemokine production / JNK cascade / signaling adaptor activity / response to interleukin-1 / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / Hedgehog 'on' state / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / positive regulation of NF-kappaB transcription factor activity / Interleukin-1 signaling / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / protein polyubiquitination / 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 / response to ethanol / molecular adaptor activity / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / gene expression / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / endosome membrane / defense response to Gram-positive bacterium / nuclear speck / defense response to bacterium / innate immune response / apoptotic process / ubiquitin protein ligase binding / positive regulation of gene expression / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding
Similarity search - Function
Myeloid differentiation primary response protein MyD88 / MyD88, death domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / TIR domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / TIR domain / MATH/TRAF 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. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Death-like domain superfamily / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Speckle-type POZ protein / Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3212
Polymers18,3212
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarization binding assay.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-5 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.830, 57.080, 61.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Speckle-type POZ protein / HIB homolog 1 / Roadkill homolog 1


Mass: 16309.796 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: O43791
#2: Protein/peptide Myeloid differentiation primary response protein MyD88


Mass: 2011.279 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.: 169 / 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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Apr 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.45→41.77 Å / Num. obs: 25391 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 15.21 Å2 / CC1/2: 1 / Net I/σ(I): 20.5
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 2472 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
Coot1.20.1_4487model building
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→33.39 Å / SU ML: 0.1411 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1222 4.81 %
Rwork0.1631 24167 -
obs0.1653 25389 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 1.45→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 0 169 1369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961233
X-RAY DIFFRACTIONf_angle_d1.02971663
X-RAY DIFFRACTIONf_chiral_restr0.0907184
X-RAY DIFFRACTIONf_plane_restr0.0082210
X-RAY DIFFRACTIONf_dihedral_angle_d5.8753164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.510.22861360.17452598X-RAY DIFFRACTION98.88
1.51-1.580.20011560.14892628X-RAY DIFFRACTION99.96
1.58-1.660.22011410.14872662X-RAY DIFFRACTION100
1.66-1.760.21581340.14672618X-RAY DIFFRACTION100
1.76-1.90.1951600.14872669X-RAY DIFFRACTION100
1.9-2.090.18851350.1472673X-RAY DIFFRACTION100
2.09-2.390.17511160.15362708X-RAY DIFFRACTION100
2.39-3.020.23521270.17632729X-RAY DIFFRACTION100
3.02-33.390.23451170.17262882X-RAY DIFFRACTION99.97

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