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- PDB-7klz: Structure of SPOP MATH domain in complex with a Geminin peptide -

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Basic information

Entry
Database: PDB / ID: 7klz
TitleStructure of SPOP MATH domain in complex with a Geminin peptide
Components
  • Geminin peptide
  • Speckle-type POZ protein
KeywordsPROTEIN BINDING / SPOP / Geminin / MATH domain / E3 ubiquitin ligase / DNA damage response / DNA replication
Function / homology
Function and homology information


DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / regulation of proteolysis / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / negative regulation of DNA replication / regulation of DNA replication ...DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / regulation of proteolysis / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / negative regulation of DNA replication / regulation of DNA replication / negative regulation of cell cycle / Activation of the pre-replicative complex / localization / regulation of mitotic cell cycle / transcription repressor complex / Assembly of the pre-replicative complex / animal organ morphogenesis / Hedgehog 'on' state / histone deacetylase binding / protein polyubiquitination / transcription corepressor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / nuclear speck / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Geminin/Multicilin / Geminin / 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. ...Geminin/Multicilin / Geminin / 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
PHOSPHATE ION / Speckle-type POZ protein / Geminin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCui, G. / Botuyan, M.V. / Mer, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
CitationJournal: Nat Commun / Year: 2021
Title: SPOP mutation induces replication over-firing by impairing Geminin ubiquitination and triggers replication catastrophe upon ATR inhibition.
Authors: Ma, J. / Shi, Q. / Cui, G. / Sheng, H. / Botuyan, M.V. / Zhou, Y. / Yan, Y. / He, Y. / Wang, L. / Wang, Y. / Mer, G. / Ye, D. / Wang, C. / Huang, H.
History
DepositionNov 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Speckle-type POZ protein
C: Geminin peptide
D: Geminin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9616
Polymers35,7714
Non-polymers1902
Water00
1
A: Speckle-type POZ protein
C: Geminin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0754
Polymers17,8862
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-3 kcal/mol
Surface area8000 Å2
MethodPISA
2
B: Speckle-type POZ protein
D: Geminin peptide


Theoretical massNumber of molelcules
Total (without water)17,8862
Polymers17,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-4 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.060, 103.060, 131.810
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVAL(chain 'A' and ((resid 28 and (name N or name...AA28 - 1645 - 141
21METMETVALVAL(chain 'B' and (resid 28 through 61 or (resid 62...BB28 - 1645 - 141
12GLUGLUTHRTHR(chain 'C' and ((resid 196 and (name N or name...CC196 - 2032 - 9
22GLUGLUTHRTHRchain 'D'DD196 - 2032 - 9

NCS ensembles :
ID
1
2

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Components

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


Mass: 16434.949 Da / Num. of mol.: 2 / 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: Protein/peptide Geminin peptide


Mass: 1450.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75496
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
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: 4.89 Å3/Da / Density % sol: 74.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.39→47.99 Å / Num. obs: 10264 / % possible obs: 99.8 % / Redundancy: 37 % / Biso Wilson estimate: 77.87 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.24
Reflection shellResolution: 3.39→3.52 Å / Rmerge(I) obs: 1.27 / Num. unique obs: 985

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F8G

6f8g


Resolution: 3.4→47.99 Å / SU ML: 0.4481 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.2103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 1026 10 %
Rwork0.2098 9238 -
obs0.213 10264 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.27 Å2
Refinement stepCycle: LAST / Resolution: 3.4→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 10 0 2307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192349
X-RAY DIFFRACTIONf_angle_d0.47923161
X-RAY DIFFRACTIONf_chiral_restr0.0389349
X-RAY DIFFRACTIONf_plane_restr0.0029395
X-RAY DIFFRACTIONf_dihedral_angle_d1.85381395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.580.32691420.27981281X-RAY DIFFRACTION100
3.58-3.80.30861430.24361288X-RAY DIFFRACTION100
3.8-4.10.28061440.23851300X-RAY DIFFRACTION100
4.1-4.510.22631450.18671298X-RAY DIFFRACTION99.93
4.51-5.160.19521460.15951315X-RAY DIFFRACTION100
5.16-6.50.22111480.19271334X-RAY DIFFRACTION100
6.5-47.990.22551580.21941422X-RAY DIFFRACTION99.37
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)
10.342173998867-0.588776260034-0.01724735374621.80344648841-0.5130364677660.3752361281060.167297271379-0.860393760037-0.1226093449940.0321789521151-0.1734474756980.2546370876660.394082445885-0.239362464996-0.05500837714840.233878811440.0789859698574-0.0004037466571660.895288530804-0.05021538661380.553053256871-19.572265109327.650683936-18.6967617411
21.11468243748-1.63877762778-2.417701045828.916995104880.8425345470339.46712841974-0.979012194311-0.371851261099-0.06928348926911.38499967129-0.526569836292-0.3332544841050.9055374378351.70550075360.9527106205870.8312970398270.0993635712208-0.02665067459721.010284666660.09400568925280.628373463675-7.3318202113725.0548801875-8.64872512177
30.6938352794690.896947291987-0.5872161614013.004223482950.2514906716791.05819579338-0.159941500244-1.100807694150.6516030067150.460957838698-0.1622791825410.33204401177-0.278110062436-0.7534215266380.4298999526380.464093792740.06188988790440.01161739384920.952266528279-0.281429249310.44920882532-21.202413373934.9014061838-11.0334080527
41.338403825450.153553685991.312348540543.172631035340.1578692194514.201519044010.0232295304119-0.9643359539140.427137774947-0.10936759392-0.0961132405780.0937998803756-0.5225897142050.4769899114490.08682277727880.491503039929-0.12736261504-0.05353191614960.937146728288-0.316676155080.811704897616-11.892066503738.4476992008-15.5211235104
50.641332739951-0.235878415076-0.7734479016172.395692269170.1937300419191.85586889803-0.263589716379-0.8038728768920.317331317593-0.1027424330440.1406730164710.430245242974-0.248480598431-0.5525460710940.1080126168180.3382237671950.146032151036-0.0987385490240.584289705672-0.2162577557390.606154963158-18.620941694535.6254873255-22.5125430189
69.455748974141.432427446144.166719081743.02051201517-1.202437421643.02116046660.635168558425-0.796284709797-0.7490695598580.073356685305-0.257462767552-0.320368242298-0.532794188699-0.838776720852-0.03747357883750.3545897250830.153900282199-0.02134133144551.0415169502-0.08614591856770.5997844065371.5881790545828.7174541142-19.7773854239
70.54481725592-0.7013225239110.6321474463551.602235255470.4474037489823.05041171627-0.2923922090660.899044282055-0.183452816498-0.2950355600750.417114273529-0.647639140571-0.489733856536-0.03969008517430.09483793665120.2571269801590.04222956041720.05983326546470.881957648938-0.06058841315790.62644755744317.153510601229.5637905094-15.9684553252
81.284823226410.252917912677-2.383937607532.06651396014-3.362048444398.57480712818-0.8045625643750.31652943343-0.962554129850.5865454613740.1042906425722.032264901091.56871056408-1.530920830560.2515629987021.05399882633-0.2972678389460.2941282917821.29984737912-0.4194456301140.951302707307-3.4700146261816.578454234-22.6089419212
93.74945802409-1.243063591010.2752647307054.911184695940.0357755612720.625013118860.3702419227791.316169623860.841756343374-0.8666526570860.027435690653-0.663607220906-0.0006105424696750.517622068951-0.2064517420310.394733986739-0.05859932145420.0866339482541.19512629172-0.04531974013070.72676702030118.134323922432.6283022258-26.5662769443
103.006670712640.2774129735880.6161831615733.67308310188-0.3352486373963.1716101925-0.3314459641961.11964090142-0.100206051458-0.6124622688720.04076841658440.839067593302-0.12846815269-0.6618633043770.3208666958290.6876393604640.111282064658-0.1521980800231.33842519678-0.09738444508680.6365372865274.5396750346231.3767470231-25.0617763758
113.246239240640.2467734422191.005918662621.77718211330.9884006222843.91554569589-0.2421202943612.639889420880.1234111745-0.89953550730.318272668776-0.173449475517-0.8573013913930.5597008961770.00266849583180.906702402904-0.00950910669174-0.1109760760541.890107394580.02919249650580.8804225250818.3690598333431.9325360637-31.6066575203
124.03053210114-0.07799440875192.423895855883.481602992220.8279560690094.73466291787-0.3019322715140.2123762697920.826396081541-0.4431555483440.02901803547080.0840581336633-0.894068163232-0.4840554043370.1483364943560.4634685938320.001443587130550.05549802292410.657767258557-0.04978997797710.4035523774869.5128924735837.8253262364-17.9191047166
131.45022955953-0.811662678678-1.640017067032.147740483260.3481649160822.672873924730.4725524304380.215218569839-0.2415498637630.0252556608599-0.4242829585160.832547452138-0.646809558757-0.4659120037970.259365884880.6576207793540.1032307705380.2400948394930.502218376392-0.4514780860591.36068979435-20.343120659842.9270911755-10.0034216894
144.62522979918-5.1694616306-2.207806179427.172763777321.298034008657.870794809811.028203755730.5229852466290.792360852916-0.541358457126-0.0568032687738-0.403695406499-1.143748247960.3708828840890.03154498184850.623115961556-0.07854146914310.2023021958251.924172933210.08637115131630.57924811680212.926417412931.7579553129-35.1510454044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 165 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 39 )
7X-RAY DIFFRACTION7chain 'B' and (resid 40 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 66 )
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 84 )
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 116 )
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 138 )
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 165 )
13X-RAY DIFFRACTION13chain 'C' and (resid 196 through 204 )
14X-RAY DIFFRACTION14chain 'D' and (resid 196 through 204 )

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