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- PDB-7liq: X-ray structure of SPOP MATH domain (S119A) -

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Basic information

Entry
Database: PDB / ID: 7liq
TitleX-ray structure of SPOP MATH domain (S119A)
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: 1.98 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


Theoretical massNumber of molelcules
Total (without water)16,4771
Polymers16,4771
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.457, 77.457, 106.246
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-254-

HOH

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Components

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


Mass: 16476.986 Da / Num. of mol.: 1 / Fragment: MATH domain / Mutation: S119A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown by the hanging drop method, mixing 2 ul of the SPOP MATH S119A at 20 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the ...Details: Crystals were grown by the hanging drop method, mixing 2 ul of the SPOP MATH S119A at 20 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.2 M (NH4)2SO4, 0.1 M BIS-Tris, pH 6.5, 25% (w/v) PEG 3,350).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.98→41.65 Å / Num. obs: 13677 / % possible obs: 99.98 % / Redundancy: 36.8 % / Biso Wilson estimate: 41.19 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.011 / Rrim(I) all: 0.068 / Net I/σ(I): 29.41
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 0.998 / Num. unique obs: 1321 / CC1/2: 0.898 / CC star: 0.973 / Rpim(I) all: 0.182 / Rrim(I) all: 1.015

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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: 1.98→41.65 Å / SU ML: 0.2437 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 1368 10 %
Rwork0.1917 12308 -
obs0.195 13676 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.36 Å2
Refinement stepCycle: LAST / Resolution: 1.98→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 64 1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951173
X-RAY DIFFRACTIONf_angle_d1.04551574
X-RAY DIFFRACTIONf_chiral_restr0.0728166
X-RAY DIFFRACTIONf_plane_restr0.0064200
X-RAY DIFFRACTIONf_dihedral_angle_d17.5559437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.050.31621330.26031188X-RAY DIFFRACTION100
2.05-2.130.28581320.22211198X-RAY DIFFRACTION100
2.13-2.230.27191350.21631205X-RAY DIFFRACTION100
2.23-2.350.2671340.21761217X-RAY DIFFRACTION100
2.35-2.50.29641340.22881198X-RAY DIFFRACTION100
2.5-2.690.27021350.21541218X-RAY DIFFRACTION100
2.69-2.960.25851360.21221222X-RAY DIFFRACTION100
2.96-3.390.22411370.19381238X-RAY DIFFRACTION100
3.39-4.270.20761410.16831266X-RAY DIFFRACTION100
4.27-41.650.1871510.17781358X-RAY DIFFRACTION100
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)
14.818129562530.890255324075-1.596561300575.537598412760.2641390399355.971260563210.0102526823072-0.0288112643567-0.1445863666190.142670387942-0.006860046151610.07354519881740.06281458095970.0682233770866-0.0154020353180.264958091237-0.07369501892980.07966323748150.282286795899-0.05639340231830.287835265382-11.604229433826.3458045451-2.3448068578
24.783151834563.26535750251-0.6482093132675.80862083285-0.512440030861.87855848307-0.0933088962495-0.1059817480450.6140922751350.1863557775110.1907817666850.146310899951-0.3340506451240.4559810512790.0008035886730920.431553939856-0.1138048908490.07575602461140.449997720284-0.04105313025630.35364260493-10.272397260928.65293336482.7098119071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 48 )

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