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- PDB-9hgg: SETD2 peptide bound to SPOP MATH domain -

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Basic information

Entry
Database: PDB / ID: 9hgg
TitleSETD2 peptide bound to SPOP MATH domain
Components
  • Histone-lysine N-methyltransferase SETD2
  • Speckle-type POZ protein
KeywordsLIGASE / Ubiquitination / Complex / Degradation
Function / homology
Function and homology information


mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / embryonic placenta morphogenesis / histone H3K36 trimethyltransferase activity / pericardium development ...mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / embryonic placenta morphogenesis / histone H3K36 trimethyltransferase activity / pericardium development / regulation of mRNA export from nucleus / stem cell development / histone H3K36 methyltransferase activity / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity / embryonic cranial skeleton morphogenesis / positive regulation of ossification / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / positive regulation of interferon-alpha production / regulation of proteolysis / alpha-tubulin binding / mismatch repair / forebrain development / positive regulation of autophagy / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / stem cell differentiation / neural tube closure / transcription elongation by RNA polymerase II / Hedgehog 'on' state / : / PKMTs methylate histone lysines / protein polyubiquitination / chromosome / regulation of gene expression / angiogenesis / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / regulation of DNA-templated transcription / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain ...SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Speckle-type POZ protein / Histone-lysine N-methyltransferase SETD2
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 Heart, Lung, and Blood Institute (NIH/NHLBI)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 POZ protein
B: Histone-lysine N-methyltransferase SETD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1827
Polymers18,0612
Non-polymers1225
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-34 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.565, 51.043, 54.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

MG

21A-203-

MG

31A-340-

HOH

41A-347-

HOH

51A-372-

HOH

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Components

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


Mass: 16283.759 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 Histone-lysine N-methyltransferase SETD2 / HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin- ...HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin-interacting protein B / Lysine N-methyltransferase 3A / Protein-lysine N-methyltransferase SETD2 / SET domain-containing protein 2 / hSET2 / p231HBP


Mass: 1776.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9BYW2, [histone H3]-lysine36 N-trimethyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.73 Å3/Da / Density % sol: 28.85 %
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 sodium fluoride, 0.03 M sodium bromide, 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→44.56 Å / Num. obs: 10343 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 23.88 Å2 / CC1/2: 0.99 / Net I/σ(I): 45.9
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 1018 / CC1/2: 0.85

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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→44.56 Å / SU ML: 0.1756 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.8991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2561 484 4.68 %
Rwork0.1942 9853 -
obs0.1973 10337 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 5 121 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241226
X-RAY DIFFRACTIONf_angle_d1.21221649
X-RAY DIFFRACTIONf_chiral_restr0.0635182
X-RAY DIFFRACTIONf_plane_restr0.0096208
X-RAY DIFFRACTIONf_dihedral_angle_d6.7532163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.170.29211670.23863189X-RAY DIFFRACTION99.85
2.17-2.740.27251520.23253264X-RAY DIFFRACTION100
2.74-44.560.24021650.16813400X-RAY DIFFRACTION99.92
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)
12.20655270746-1.337061060420.6407030644442.28407382865-0.4658995569112.47937485868-0.234437202824-0.2310337546810.278626946024-0.04669339563160.0614680791527-0.1515359697520.02992772586510.1145423990260.1295950895680.168304949037-0.02554726812380.04102383012140.266709587651-0.005577254556530.11709375217716.183189935919.66137181615.60882168066
22.7935684426-0.504723826178-1.581538585023.46644288308-0.3441612309253.496039015850.11769407244-0.4032612556740.194349270543-0.122299792199-0.138135239647-0.344226876433-0.1124941163890.5203198416930.005322601786520.208008149955-0.01280535433470.04231342634670.291674617401-0.002070992028880.16535194565821.857977418.5741175857-0.951788372334
33.952611018614.279089885190.3296793635665.251328559981.438257426882.19120600658-0.518747055491.21460283510.322112295291-0.5111015161390.594680471710.271599275578-0.106121724420.157261600221-0.1597652865960.266547939854-0.0201132780953-0.04833211305850.2671707352880.04230643928780.1823888532219.921585723515.67019176420.603611587239
46.02598386727-1.02061014265-0.142623152584.538255144760.1346909586848.88486736069-0.418603453025-0.0271607162115-1.01035928257-0.07920436879740.05269142722710.3952389216470.943154620319-0.6469272610620.2433153324790.220170913467-0.09256037995990.08023540655290.328531417095-0.03589216892690.3796523272535.159694450056.632159528345.34636416312
54.513522787251.37046970928-2.332034420952.50030560882-0.6741297905723.10128225053-0.08793838059980.42732713481-0.723906452675-0.170225234228-0.131138649396-0.3101532628060.3236620886630.5406884835780.1847179548460.1551236787420.05131407575990.006603279111450.345784920055-0.02668924020420.19064248652826.345920505711.79265697440.123541427799
64.85485391085-2.6453086183-3.539524469265.164130873191.825108904585.74030452264-0.672612290736-0.4000474380020.5052381155630.5092610634090.409290487289-0.7222082280310.4436743167370.9291492195090.1745515380260.2094903049890.0489600693912-0.04371532722790.2564437731160.003387661126040.1804520571524.380907905213.260773174910.6418829004
75.30843566202-2.551539111981.071227184122.51552151390.3218091448468.48735717060.0782135749426-0.2859684677160.2659593936890.177776089252-0.050590371042-0.996985792556-0.4650400195321.19630073473-0.03367907790270.174690665719-0.04952057842-0.02334942592380.2399321545980.04147343914670.20845411405312.552238605822.882507619418.8093950058
83.55189442759-1.26235603039-2.49820360371.93417231619-0.2867211801645.237714670550.0499488146155-0.4671770335290.1039515867420.1679429513830.3520225484150.1009918117130.269203247030.478660547513-0.3868749423130.1981797308450.000233161912847-0.02524645847560.2528263456560.009394808575680.18468780907426.1287198947.578467692926.75734213131
95.10714376298-1.98835256229-1.463182728462.74922622771.561553947284.03140870286-0.236247690327-0.362705240618-0.492078608460.1275638803360.08386904120830.4404699015250.143037041179-0.4316222304290.1920592404850.186750030222-0.01754107577150.01538188791060.2237816144640.05523388566120.2148933645647.6781281713712.998118066311.698315505
102.80311861087-1.47667645102-1.456610883783.326952626250.7104449988832.447864540160.03633488451350.04775066333320.5714866534690.0580116789026-0.0711851529871-0.234848736894-0.1843257257520.279305860149-0.01766534053050.133200295115-0.0101339900028-6.55173954193E-50.1727878088840.002275454080140.11335717832618.349635166320.60186801839.88468642694
115.33095296627-1.0217774801-1.600978737694.309886485912.48609878486.75580827415-0.2248715082990.0701384198389-0.8234132257110.2899898075950.06674094753060.2813502995350.5812798125860.1572964350710.1671632556830.267125504024-0.01877292494230.003667662806740.1234310825740.01185118293370.31329731867813.55318063635.2245829771810.3768008321
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 48 )AA26 - 481 - 23
22chain 'A' and (resid 49 through 65 )AA49 - 6524 - 37
33chain 'A' and (resid 66 through 72 )AA66 - 7238 - 44
44chain 'A' and (resid 73 through 84 )AA73 - 8445 - 56
55chain 'A' and (resid 85 through 97 )AA85 - 9757 - 69
66chain 'A' and (resid 98 through 106 )AA98 - 10670 - 78
77chain 'A' and (resid 107 through 116 )AA107 - 11679 - 88
88chain 'A' and (resid 117 through 129 )AA117 - 12989 - 101
99chain 'A' and (resid 130 through 147 )AA130 - 147102 - 119
1010chain 'A' and (resid 148 through 166 )AA148 - 166120 - 138
1111chain 'B' and (resid 1364 through 1377 )BB1364 - 13771 - 14

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