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- PDB-9hfw: SRC-3 (NCoA-3) peptide bound to SPOP MATH domain -

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Basic information

Entry
Database: PDB / ID: 9hfw
TitleSRC-3 (NCoA-3) peptide bound to SPOP MATH domain
Components
  • Nuclear receptor coactivator 3
  • Speckle type BTB/POZ protein
KeywordsLIGASE / Ubiquitination / Complex / Degradation
Function / homology
Function and homology information


: / cell dedifferentiation / regulation of stem cell division / positive regulation of keratinocyte differentiation / vitamin D receptor signaling pathway / nuclear thyroid hormone receptor binding / histone acetyltransferase activity / positive regulation of stem cell population maintenance / RNA polymerase II complex binding / retinoic acid receptor signaling pathway ...: / cell dedifferentiation / regulation of stem cell division / positive regulation of keratinocyte differentiation / vitamin D receptor signaling pathway / nuclear thyroid hormone receptor binding / histone acetyltransferase activity / positive regulation of stem cell population maintenance / RNA polymerase II complex binding / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / nuclear receptor binding / cellular response to estradiol stimulus / protein catabolic process / PPARA activates gene expression / MAPK6/MAPK4 signaling / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / disordered domain specific binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Estrogen-dependent gene expression / transcription coactivator activity / protein dimerization activity / chromatin / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking ...: / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / BTB/POZ domain / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / BTB domain profile. / PAS domain / BTB/POZ domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / SKP1/BTB/POZ domain superfamily / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Speckle type BTB/POZ protein / Nuclear receptor coactivator 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.0Apr 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: Nuclear receptor coactivator 3


Theoretical massNumber of molelcules
Total (without water)17,8772
Polymers17,8772
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-7 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.039, 54.282, 45.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-244-

HOH

21A-283-

HOH

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Components

#1: Protein Speckle type BTB/POZ protein


Mass: 16141.605 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 Nuclear receptor coactivator 3 / NCoA-3 / ACTR / Amplified in breast cancer 1 protein / AIB-1 / CBP-interacting protein / pCIP / ...NCoA-3 / ACTR / Amplified in breast cancer 1 protein / AIB-1 / CBP-interacting protein / pCIP / Class E basic helix-loop-helix protein 42 / bHLHe42 / Receptor-associated coactivator 3 / RAC-3 / Steroid receptor coactivator protein 3 / SRC-3 / Thyroid hormone receptor activator molecule 1 / TRAM-1


Mass: 1735.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y6Q9, histone acetyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.85 Å3/Da / Density % sol: 33.41 %
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 sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 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: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Dec 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.7→45.88 Å / Num. obs: 15071 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 13.85 Å2 / CC1/2: 1 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 1420 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.88 Å / SU ML: 0.171 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 808 5.36 %
Rwork0.1779 14259 -
obs0.1803 15067 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.72 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 0 132 1316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121235
X-RAY DIFFRACTIONf_angle_d1.12391668
X-RAY DIFFRACTIONf_chiral_restr0.063184
X-RAY DIFFRACTIONf_plane_restr0.0097212
X-RAY DIFFRACTIONf_dihedral_angle_d6.2668167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.26481440.22112281X-RAY DIFFRACTION98.18
1.81-1.950.21731370.18042324X-RAY DIFFRACTION100
1.95-2.140.21321300.17892346X-RAY DIFFRACTION100
2.14-2.450.22761280.16752391X-RAY DIFFRACTION100
2.45-3.090.23761460.18632379X-RAY DIFFRACTION99.92
3.09-45.880.20641230.16872538X-RAY DIFFRACTION99.81
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)
11.91923321492-0.0817301284838-2.445228802852.008546645380.3205016490524.2612138046-0.04553051646960.755527503517-0.274056689148-0.287457502998-0.1251561220310.0594884276437-0.113998448972-0.2152006147690.2573788703840.0798896237109-0.00298100577772-0.008435400183880.261492689077-0.04941114036630.1118150765873.320850641596.698864692620.751303950213
26.41898099836-0.172905826685-0.3171050676992.852048999470.4915525251811.82442005905-0.00187801800908-0.836229835328-0.4150747486660.3819615107180.1776988703140.2586829942670.0800983567808-0.0480084906204-0.1049412673920.1492677752750.02406920541760.03313407908530.1930296051650.08312422468140.2189446693927.97405029104-0.24498790947918.9921567113
34.35249572650.4370554926822.440438753721.268710910911.143724982183.320245381260.1406468964620.113346084309-0.485608892277-0.029840728593-0.09907853635160.1902444178210.3242165815-0.57449205238-0.3572448163960.0491897247447-0.0172656537490.009687831287890.195666293241-0.05575255962820.1849891007077.48627084255-1.225385826574.79782225551
42.362846700850.7502412389251.814607856332.708210162640.9854430460912.572433048180.1208485755280.155463120754-0.176630549551-0.427698990433-0.009366711809670.167281042560.00308735002169-0.512762108407-0.01821888451440.1141698728620.0353783723006-0.01210075074180.191696646845-0.04699761890080.1232146076637.960862518121.14212706372-4.3716407539
57.294691399820.1239613422533.091089286655.812793767292.447846460797.7549934664-0.098632130365-0.356752137522-0.2254350906680.1113126298110.173332871833-0.3338246696930.1113429862420.240280705083-0.021198824760.08282079395290.0324633341886-0.004033152493420.1340329602230.01785656180810.0752320431219.12589160054.3325956297816.4360989287
61.340100925170.07704080774860.8101351707595.13755486876-1.337583830272.621647473550.03307364756060.117118804613-0.139451821227-0.89614425464-0.0399144721443-0.2438528260380.138979819020.276301125147-0.3659833471970.03253331023420.009796321709470.03339503281810.125301185722-0.01990910856860.071090115496214.2787181027-0.155369281318-4.83542006651
76.3524145148-2.46866950597-4.272623362264.555515467123.200955056723.931120546270.1496347224010.1780580497920.289177818889-0.4017418343230.0269153282183-0.194139988488-0.2888733288520.0573504565067-0.2475660341410.08783436186720.0081727059418-0.007043840303950.0876592787665-0.006305329942330.052222658235613.032256748110.4923010669-2.20934558064
82.87816099337-0.877981365388-4.313942326724.159056365430.3355134226447.076678540670.0466870468866-0.1424779583530.281824460301-0.1219445123020.1092772450120.340128510138-0.518338281852-0.275982184626-0.1590718598060.1260451410470.0351680480591-0.0202693851860.109673163395-0.00115264578880.1161537446173.304283564818.63374138459.84187318044
93.130331867550.688951378568-0.7381469068690.8216951278930.03403134818274.303216363050.1744393062560.129728352792-0.0139537915147-0.450861405135-0.142480118489-0.39332784697-0.32969331950.209274692039-0.10502086440.08345325642550.0174980823830.03709717467260.1150684690560.0001894516802840.070770686806818.63440037117.05781696574-3.81999378377
102.36686374272-1.59265022188-1.24229955412.879762442711.447432486752.59093687386-0.189522287009-0.270932026436-0.0171214082190.3166050784650.166866648693-0.01578080352280.02450955308710.2515340298790.05524173850820.05630139306160.00152880132157-0.004573111637020.09516543246640.01726003047620.062406533325713.718444247611.004931344813.9133271686
111.32594442898-0.807135867299-1.647816127372.667557974361.725289863488.04422968741-0.06842767164540.0936121695631-0.0934361006091-0.003957390203680.03498397708010.1838476832340.0755194656426-0.134738554721-0.029566617180.008011074221550.000786730777792-0.03772859742850.0837746992283-0.01214562559860.0899446755994.339350167910.19368627667.00321203559
121.668079695350.643526308632-0.5842513167313.296719283331.540362999493.84735030880.0185334457666-0.2597066195040.1137928243830.4482410409810.385829758201-0.709805958771-0.07160737259370.677498405541-0.4141674957380.130404765291-0.0199373961562-0.05519071645390.228369798579-0.03026372616960.17237097408221.738797905111.761125674510.8398775085
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 38 )AA30 - 381 - 9
22chain 'A' and (resid 39 through 48 )AA39 - 4810 - 19
33chain 'A' and (resid 49 through 58 )AA49 - 5820 - 29
44chain 'A' and (resid 59 through 72 )AA59 - 7230 - 43
55chain 'A' and (resid 73 through 84 )AA73 - 8444 - 55
66chain 'A' and (resid 85 through 97 )AA85 - 9756 - 68
77chain 'A' and (resid 98 through 106 )AA98 - 10669 - 77
88chain 'A' and (resid 107 through 116 )AA107 - 11678 - 87
99chain 'A' and (resid 117 through 129 )AA117 - 12988 - 100
1010chain 'A' and (resid 130 through 147 )AA130 - 147101 - 118
1111chain 'A' and (resid 148 through 164 )AA148 - 164119 - 135
1212chain 'B' and (resid 91 through 104 )BB91 - 1041 - 14

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