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- PDB-7lio: X-ray structure of SPOP MATH domain (S119D) in complex with a 53B... -

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Basic information

Entry
Database: PDB / ID: 7lio
TitleX-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide
Components
  • Speckle-type POZ protein
  • TP53-binding protein 1 peptide
KeywordsPROTEIN BINDING / SPOP / 53BP1 / DNA damage response / Homologous recombination / Ubiquitin ligase
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / histone H4K20me2 reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / telomeric DNA binding ...ubiquitin-modified histone reader activity / histone H4K20me2 reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / telomeric DNA binding / : / histone reader activity / SUMOylation of transcription factors / regulation of proteolysis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of double-strand break repair via homologous recombination / DNA damage checkpoint signaling / replication fork / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / Hedgehog 'on' state / protein homooligomerization / G2/M DNA damage checkpoint / kinetochore / double-strand break repair via nonhomologous end joining / protein polyubiquitination / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / nuclear speck / nuclear body / DNA damage response / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
MATH domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : ...MATH domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / breast cancer carboxy-terminal domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SKP1/BTB/POZ domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
Speckle-type POZ protein / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
C: TP53-binding protein 1 peptide
B: Speckle-type POZ protein
D: TP53-binding protein 1 peptide


Theoretical massNumber of molelcules
Total (without water)35,8274
Polymers35,8274
Non-polymers00
Water00
1
A: Speckle-type POZ protein
C: TP53-binding protein 1 peptide


Theoretical massNumber of molelcules
Total (without water)17,9132
Polymers17,9132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-2 kcal/mol
Surface area7540 Å2
MethodPISA
2
B: Speckle-type POZ protein
D: TP53-binding protein 1 peptide


Theoretical massNumber of molelcules
Total (without water)17,9132
Polymers17,9132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-3 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.592, 103.592, 130.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 16520.996 Da / Num. of mol.: 2 / Fragment: MATH domain / Mutation: S119D
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 TP53-binding protein 1 peptide / p53BP1


Mass: 1392.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12888

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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: 4.89 Å3/Da / Density % sol: 74.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM ...Details: SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample 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 0.5 ml of 2 M (NH4)2SO4.

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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: 3.01→48.65 Å / Num. obs: 14508 / % possible obs: 98.9 % / Redundancy: 31.5 % / Biso Wilson estimate: 100.44 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.026 / Rrim(I) all: 0.145 / Net I/σ(I): 33.55
Reflection shellResolution: 3.01→3.11 Å / Rmerge(I) obs: 2.095 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 1368 / CC1/2: 0.74 / Rpim(I) all: 0.372 / Rrim(I) all: 2.13

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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: 3.01→48.65 Å / SU ML: 0.4497 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2766 1451 10 %
Rwork0.2283 13057 -
obs0.233 14508 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.96 Å2
Refinement stepCycle: LAST / Resolution: 3.01→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 0 0 2140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062186
X-RAY DIFFRACTIONf_angle_d0.98082969
X-RAY DIFFRACTIONf_chiral_restr0.0701340
X-RAY DIFFRACTIONf_plane_restr0.0038377
X-RAY DIFFRACTIONf_dihedral_angle_d13.1969732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.110.3641370.36291229X-RAY DIFFRACTION94.53
3.11-3.240.36541430.31941289X-RAY DIFFRACTION100
3.24-3.390.36171420.30141282X-RAY DIFFRACTION100
3.39-3.560.35711460.2641306X-RAY DIFFRACTION100
3.56-3.790.31721430.25521297X-RAY DIFFRACTION100
3.79-4.080.27161460.23781303X-RAY DIFFRACTION100
4.08-4.490.25231450.19761316X-RAY DIFFRACTION100
4.49-5.140.21721470.16931317X-RAY DIFFRACTION99.86
5.14-6.470.21951500.20361352X-RAY DIFFRACTION99.93
6.47-48.650.30191520.24091366X-RAY DIFFRACTION94.88
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)
13.81045245686-0.169341706676-5.514324420624.9057479518-2.602696058619.102582425530.530747582383-1.214863703021.497635810410.338780952102-0.007299338111710.156522372852-0.979635915141.15272214132-0.3822305502570.2870474576090.07283370640630.06940803054831.013595899250.01566036974610.944146403548-41.60071273222.9574291737-17.1090128041
26.992622739063.056480774242.159888620237.00892545955-2.005046190845.51333639868-0.0440008058592-1.65378467630.4468570221480.436708522833-0.0636376205247-0.3685110933430.2504689888420.04798404021390.1742288982460.4907802285360.0974486575348-0.02298941543950.753557637120.07922513731960.731787675255-32.480924291725.471434298-14.2740399091
37.12623654591-4.7397894839-1.017845323347.57522204112.338621691267.214301443090.141738009627-1.200625923270.6280492369621.174543696490.341252047116-1.654796067210.9376899308551.26370345167-0.2643427488310.754963036104-0.0332924042066-0.0992717009890.8762039036860.2695680186261.0970518115-30.237145746815.9208351362-10.3000918294
42.00952211080.6050154325274.145703572526.118252097890.2617283311459.05557228643-0.0478343616319-1.62693850473-0.8627570367970.340703749910.1718477430710.2426994698450.895637816869-1.88854371101-0.1102284640620.612536907065-0.01242887770960.1082281891321.352258600690.4156360725271.26692929791-39.933167723813.4193523816-15.0936449194
54.341909652673.67906357377-6.053388354899.10873391969-6.232699891928.728870148110.48444421093-1.74441200412-0.8248562011170.1601016887061.694182981091.725141928570.6617272682450.0473569347425-1.201753408430.4476663676410.1718197039750.1125095658740.9698297893570.3417195330740.998956707571-31.043606873111.5724174505-15.0480402701
62.12326556371-1.30593101753-1.077299550092.711829047462.647509141642.575627349980.518129280556-0.270832699773-0.358048014233-1.195661267330.923073976959-0.8447721271290.5307088379170.428374473619-1.348747876870.720390939572-0.05756760878980.005857526496850.6525865675830.06849029317771.14219796737-27.454701852815.548308753-30.6972918481
76.07926764413-2.30159424752-2.883167879668.52172681435-0.8118757363434.487651046770.190551214910.432252418818-0.01124973855890.2930653874680.7347437545870.503252236708-0.88399298143-1.2853202591-1.154571604940.393254960606-0.0664559649019-0.04571398689370.6650448692230.09127309175770.785660796511-38.811903363820.6318066628-20.67617763
87.84350048287-2.795072179531.62246091659.440037983320.2001320797136.199002384211.13877950668-0.597677678871-0.7860417297680.9421066734950.679505587911.47588798049-0.422382871535-1.49055963594-1.340621630690.9599409019520.5743679201490.3736815164320.6984309696351.021280560952.42244926126-33.21765267247.04501721733-9.38817470547
96.070930351283.88942051999-7.129650559153.12562694417-3.66205951527.040478556740.43353877596-0.9742550455650.3911871487180.605724273974-0.147071442119-0.490572829161-0.08671773107350.54481477846-0.3478280626340.4557180558240.05544860038380.1930817313570.9135239363880.1125748607971.09948128234-60.848404976824.1136233536-17.8014834875
105.94313610013-1.213482591670.9391112639463.333319804264.973637131738.546002106150.06550952896520.9008711318270.180487524441-1.19834239532-0.7383770988930.620958761812-0.103704840274-1.650801424490.5700852813970.7368553936850.08151826698140.09367627097341.037533342770.1640555133610.86048968985-64.605412559723.4396865168-27.7197313522
119.260417327265.13467648527-6.447018856977.4992820965-6.362267567416.32322956849-1.609784631670.676100591984-0.708406172601-1.449982094150.16246419382-1.58675914041.866291083980.4443743748841.217618978281.100223788870.143221479730.3899948669581.17103114677-0.03633606350421.07157237671-57.651608704617.8194234632-27.4206454094
127.28257322597-6.00198021508-1.2208404376.570146834845.020731128562.00525859951-0.2191655685790.632469695612-2.98913572468-4.12688030735-1.549880918330.7404031659220.475671481475-2.736451555051.65134146851.37592058238-0.06257615456140.4795918402690.903838486611-0.3963392693432.15583370213-70.75378705467.88271813718-18.9036937091
134.618759263895.37702839987-2.545941636946.76677916633-4.632276102095.10666089336-0.998073688261-0.600035393695-2.61519782136-0.833376474885-0.483075178539-1.778945328012.260787683831.812495705891.647563024940.9330003441430.3258720830640.3389288655371.069867415490.3021553816061.22380737188-59.66259107714.1666012052-16.4880500879
145.143148417633.42668662756-1.824775922268.219212169622.995929229152.000349634710.1871261813611.311700471540.5021216662940.108216202958-2.082858987421.41011598445-2.32043952578-3.655340482681.95064017451.26343871739-0.2223066574490.2388241777312.06886928219-0.9038981686351.05780562925-63.454026554419.8038949052-35.5915208947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 150 )
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 164 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1638 through 1644 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 97 )
11X-RAY DIFFRACTION11chain 'B' and (resid 98 through 138 )
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 143 )
13X-RAY DIFFRACTION13chain 'B' and (resid 144 through 164 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1639 through 1645 )

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