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- PDB-7lip: X-ray structure of SPOP MATH domain (D140G) -

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Basic information

Entry
Database: PDB / ID: 7lip
TitleX-ray structure of SPOP MATH domain (D140G)
ComponentsSpeckle-type POZ protein
KeywordsPROTEIN BINDING / SPOP / 53BP1 / DNA damage response / Homologous recombination / Ubiquitin ligase
Function / homology
Function and homology information


regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBotuyan, M.V. / Cui, G. / Mer, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM116829 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136262 United States
CitationJournal: Sci Adv / Year: 2021
Title: ATM-phosphorylated SPOP contributes to 53BP1 exclusion from chromatin during DNA replication.
Authors: Wang, D. / Ma, J. / Botuyan, M.V. / Cui, G. / Yan, Y. / Ding, D. / Zhou, Y. / Krueger, E.W. / Pei, J. / Wu, X. / Wang, L. / Pei, H. / McNiven, M.A. / Ye, D. / Mer, G. / Huang, H.
History
DepositionJan 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Speckle-type POZ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6273
Polymers16,4351
Non-polymers1922
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.766, 43.450, 51.026
Angle α, β, γ (deg.)90.000, 123.217, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

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


Mass: 16434.949 Da / Num. of mol.: 1 / Fragment: MATH domain / Mutation: D140G
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4. Two ul of the protein at 24 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT was mixed ...Details: Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4. Two ul of the protein at 24 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT was mixed with 2 ul of the reservoir solution. The reservoir solution was 0.5 ml.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.48→21.32 Å / Num. obs: 25043 / % possible obs: 95.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 15.92 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.032 / Rrim(I) all: 0.091 / Net I/σ(I): 20.56
Reflection shellResolution: 1.48→1.53 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.24 / Num. unique obs: 2391 / CC1/2: 0.87 / CC star: 0.96 / Rpim(I) all: 0.26 / Rrim(I) all: 0.72

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.16_3549phasing
Cootmodel building
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LIN

7lin


Resolution: 1.48→21.32 Å / SU ML: 0.1457 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2052 2012 8.04 %
Rwork0.1804 23025 -
obs0.1823 25037 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.54 Å2
Refinement stepCycle: LAST / Resolution: 1.48→21.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 10 146 1200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781098
X-RAY DIFFRACTIONf_angle_d0.9771483
X-RAY DIFFRACTIONf_chiral_restr0.0911161
X-RAY DIFFRACTIONf_plane_restr0.0056184
X-RAY DIFFRACTIONf_dihedral_angle_d14.2442404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.26991360.26181562X-RAY DIFFRACTION91.05
1.52-1.560.27031480.23591607X-RAY DIFFRACTION94.97
1.56-1.60.29371310.22231651X-RAY DIFFRACTION96.53
1.6-1.650.24461450.20491633X-RAY DIFFRACTION96.74
1.65-1.710.25281380.19351659X-RAY DIFFRACTION96.72
1.71-1.780.21071500.19151647X-RAY DIFFRACTION97.14
1.78-1.860.20431450.17981673X-RAY DIFFRACTION97.48
1.86-1.960.19931390.16761659X-RAY DIFFRACTION97.45
1.96-2.080.19531560.16381689X-RAY DIFFRACTION97.93
2.08-2.240.18551450.16551669X-RAY DIFFRACTION98.32
2.24-2.470.18121500.17131681X-RAY DIFFRACTION98.23
2.47-2.830.21520.17861698X-RAY DIFFRACTION98.2
2.83-3.560.18411460.16491663X-RAY DIFFRACTION95.87
3.56-21.320.21551310.18721534X-RAY DIFFRACTION86.72
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)
11.55901125542-0.115498229902-1.702780987051.222951709470.1070259017572.19223563471-0.04115982939440.000940809469704-0.02746565064420.00837035374020.08439380559910.006403575269110.2531825270440.192596179238-0.04361461590320.188004554336-0.0161040958313-0.02013555005930.1635176065620.01138347259180.147468523503-16.848816667-8.6355845641915.3989474587
29.054829268210.452817647667-0.05395761301412.139477143491.088277124842.94145981173-0.1771861744970.4085317965110.201553033761-0.2604212292740.180441388430.0283048941141-0.09057589719350.0404557561404-0.003637376531050.293603074732-0.0126704082961-0.02445444479320.158090983486-0.002050649658130.13990672786-20.4315244255-7.51489258833-4.30607369972
32.73695657329-0.4608413444431.011334079093.99310788955-1.57811676755.996814204980.0859284718664-0.203646551526-0.2593322792460.0690680740457-0.0105384233079-0.03215813028030.4822207965250.0119102820177-0.1014386576840.177970246067-0.00947023565892-0.009654911504520.1188999285710.01223796987940.147591951976-23.8226237042-13.491163279611.8389573022
41.6603854440.663857000482-0.7585174632063.94491985128-1.710453372184.788058561980.05903286143050.2456700572680.109786533802-0.294711317866-0.05793152235020.282188037521-0.08661434931870.00184513632221-0.1155900218470.19680461128-0.000911430207156-0.0312721789620.1351552389440.0007331613856360.149654544418-27.7020519805-3.496740986214.49825633805
54.06651869991-0.597585286394-0.9046916272352.230221119791.546529226532.65685812926-0.0793448022549-0.269713733846-0.2234098496610.1480268281290.05752984992520.3690461966630.515239080924-0.2658642087760.01637528796240.213774861509-0.0290166230926-0.008889084648480.1811723461480.009304202179940.177668961743-30.0023624207-11.179379151417.1141531599
63.469551967711.56541685468-2.378195392723.55893420148-1.286624837084.24203246476-0.00111152029478-0.1246375615430.01472895122950.0536937178832-0.00442519848539-0.0924923635834-0.127541407690.178082675984-0.0632646660570.1947207141150.011258466138-0.02766610931070.152861237977-0.007777626329850.152555851435-17.68218645880.33488254426215.1236176689
73.717833367120.893794636188-1.173312495089.26007522460.6228683419934.20973719830.0581326945233-0.1967758387440.2383264726860.227291835365-0.09338885592310.954902034703-0.12354506147-0.2232380961780.03807606206940.1606143830590.0438849981009-0.02669874129070.1817351109440.005314900212770.191693645275-31.1338414829-3.1459498877519.6060487812
86.14346301066.21153989834-5.547204338836.80454882947-5.873706930645.154997096190.0548962014450.07035971702850.2456272182390.01437410701040.1148742463350.38691353385-0.167613753285-0.162421239405-0.1457187609930.2048722047970.0178145167348-0.01120239592390.1469934205610.01397463024960.172257454526-27.76651394981.334682383648.89776987396
92.102474601042.193690513191.032218983683.13944358580.385883331522.68924858571-0.05462235855240.283352684627-0.259374982518-0.02894962676990.0421557985604-0.153657657780.1290921619850.0781639824255-0.03388774531430.258418146629-0.00934187440767-0.02651840665040.1530890680330.004164247413070.177183870439-15.71994151034.85859500949-1.58459887297
104.492274925332.01778470028-4.675245985492.23752605976-2.884551250749.261862470210.0720671165462-0.0564765188940.15107781119-0.03767671875060.005876984555730.042333759568-0.06692450230520.0376139725197-0.07011870106290.1436520069950.00521944671135-0.02442790439810.1182036131960.002399068136690.13607106337-14.9741055827-3.8507624257210.6985073988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 84 )
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 97 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 116 )
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 129 )
8X-RAY DIFFRACTION8chain 'A' and (resid 130 through 138 )
9X-RAY DIFFRACTION9chain 'A' and (resid 139 through 147 )
10X-RAY DIFFRACTION10chain 'A' and (resid 148 through 164 )

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