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- PDB-8q06: EF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A -

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Basic information

Entry
Database: PDB / ID: 8q06
TitleEF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A
Components
  • UV excision repair protein RAD23 homolog A
  • Ubiquitin carboxyl-terminal hydrolase MINDY
KeywordsHYDROLASE / DUB / Deubiquitylase / Deubiquitinase / ubiquitin / MINDY / RAD23 / RAD23A / UBL / EF-hand
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / histone H4K20 demethylase activity / protein K48-linked deubiquitination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / K48-linked deubiquitinase activity / UV-damage excision repair / ubiquitin-specific protease binding / proteasome binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication ...regulation of proteasomal ubiquitin-dependent protein catabolic process / histone H4K20 demethylase activity / protein K48-linked deubiquitination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / K48-linked deubiquitinase activity / UV-damage excision repair / ubiquitin-specific protease binding / proteasome binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / nucleotide-excision repair / ubiquitin binding / protein destabilization / DNA Damage Recognition in GG-NER / kinase binding / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / cysteine-type deubiquitinase activity / ubiquitinyl hydrolase 1 / Golgi apparatus / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Deubiquitinating enzyme MINDY-3/4, conserved domain / Deubiquitinating enzyme MINDY-3/4 / Deubiquitinating enzyme MINDY-3/4, conserved domain / DUF4205 / RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding ...Deubiquitinating enzyme MINDY-3/4, conserved domain / Deubiquitinating enzyme MINDY-3/4 / Deubiquitinating enzyme MINDY-3/4, conserved domain / DUF4205 / RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / EF-hand domain pair / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase MINDY / Lysine-specific demethylase RAD23A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArmstrong, L.A. / Kulathu, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: EF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A
Authors: Armstrong, L.A. / Kulathu, Y.
History
DepositionJul 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 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: Ubiquitin carboxyl-terminal hydrolase MINDY
B: Ubiquitin carboxyl-terminal hydrolase MINDY
C: UV excision repair protein RAD23 homolog A
D: UV excision repair protein RAD23 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5895
Polymers37,4974
Non-polymers921
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.279, 134.139, 45.498
Angle α, β, γ (deg.)90.000, 114.670, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase MINDY


Mass: 8840.046 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MDA_GLEAN10008107 / Production host: Escherichia coli (E. coli) / References: UniProt: L5MDV7, ubiquitinyl hydrolase 1
#2: Protein UV excision repair protein RAD23 homolog A / HR23A / hHR23A


Mass: 9908.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RAD23A / Production host: Escherichia coli (E. coli) / References: UniProt: P54725
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium chloride, 2.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→34.78 Å / Num. obs: 32714 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.67 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05579 / Rpim(I) all: 0.02277 / Rrim(I) all: 0.06032 / Net I/σ(I): 19.63
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.6422 / Num. unique obs: 3242 / CC1/2: 0.919 / CC star: 0.979 / Rpim(I) all: 0.2734 / Rrim(I) all: 0.699 / % possible all: 99.48

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.78 Å / SU ML: 0.2514 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.3824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2471 1593 4.87 %
Rwork0.1966 31106 -
obs0.199 32699 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 6 159 2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382409
X-RAY DIFFRACTIONf_angle_d0.833254
X-RAY DIFFRACTIONf_chiral_restr0.0497373
X-RAY DIFFRACTIONf_plane_restr0.0076423
X-RAY DIFFRACTIONf_dihedral_angle_d6.5868314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.33911600.30132767X-RAY DIFFRACTION99.42
1.96-2.030.31631690.26722781X-RAY DIFFRACTION99.9
2.03-2.110.29751480.24852823X-RAY DIFFRACTION99.9
2.11-2.210.25681400.21942832X-RAY DIFFRACTION100
2.21-2.330.26161130.20722840X-RAY DIFFRACTION100
2.33-2.470.26541610.22162805X-RAY DIFFRACTION100
2.47-2.660.27031580.22542864X-RAY DIFFRACTION100
2.66-2.930.32921180.23942834X-RAY DIFFRACTION99.97
2.93-3.350.26611500.22792825X-RAY DIFFRACTION100
3.35-4.220.2311510.16792852X-RAY DIFFRACTION100
4.22-34.780.19181250.15852883X-RAY DIFFRACTION99.83
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)
16.57461134228-0.283289166584-0.2573051685979.53864570586-0.008287268810564.59329887230.2865955666260.212456646357-0.780104958217-0.45867599308-0.0530615580557-0.07187996136220.542364658507-0.00460208718681-0.2830996607990.380348857076-0.0441722334657-0.1333239542240.3270027184970.04133599794360.4736995760248.8438436392512.692178288511.609139729
24.33035309504-1.585997425891.096203491134.52548598738-1.236378463787.061790213120.2499161733730.1129812399490.244885916976-0.0683022515029-0.288630425477-0.405066990018-0.1939906374060.541710108995-0.006030083523380.412843438242-0.0378438432551-0.01545867430980.3333193001380.04904818157640.37201210596911.671799932824.031625092814.5777616428
33.965160726135.82093884428-0.8799428967789.75939725246-1.860620567687.90274068139-0.147559769815-0.7826615874710.2823086088110.63416339413-0.1498761297350.329825214011-0.8158905791860.2274756480460.2737217965710.657745925657-0.02948488699330.09126098801190.3309376769010.01639211414120.3246661164445.25883443331.693934579614.1745792569
46.59126760337-3.41752135604-4.774651220577.251356233063.135055400198.527786315050.5933852241670.269192695325-0.245853078832-0.170583562358-0.4374394733480.196150822093-0.435383894613-0.520300070796-0.1960020822190.466250271063-0.04183372669020.004796223388490.2749429525920.05639823815350.3525823347720.99517363887222.596192045212.9413677535
50.9662889408370.5993477016210.3327837819163.516843158063.875121245413.98573052712-0.306801307936-0.0307406775576-0.0216207854618-0.0153626972754-0.3633187765280.44353317475-0.872978172419-0.335157088950.4801612431470.522047325360.03364218571980.09352281475050.3824470843580.07086232753410.42645091990630.036184966623.63403038228.5458105528
68.467591106390.2680689139412.417128905196.11613808599-0.1873233413447.373861779090.2860952657720.714477343807-0.0558149411293-0.222218409501-0.1322490617810.0556821625906-0.0971106180519-0.154198794815-0.07851812916920.4464176357760.08006951895320.01702639916790.417383197446-0.01770592551410.39578911208128.588378648314.637831287115.836048029
77.140872282460.4269622420760.5627439940963.09099222897-1.77456386618.375832424710.04936465423270.127422392513-0.822549158676-0.587716585374-0.0694521261668-0.2107552307250.524583045876-0.0902087124637-0.04876283409990.3847996105790.0184609782537-0.04630955399660.3635970115640.02846898506110.43332122475925.80354933644.6873517529723.7034374793
85.32885784219-0.4539138652462.41470552595.58488921109-2.595641420498.282352403120.4132394188040.16786274396-0.0274384221948-0.388724872799-0.1214465141280.5126890481480.181373292662-0.634578504015-0.2493986160540.3715681160220.0822340816799-0.06751574694510.418973682143-0.009562715517830.41206049228219.357177934812.764104483620.2961544978
9-0.0454533654701-0.035720997646-0.08018453323143.574526080614.811674299776.777753027350.3049598676270.09248828511380.379487030967-0.763063068427-0.6625602945570.156045881233-0.338701184437-1.943918328660.5897445025630.520802774488-0.098558990071-0.07637643221690.654876000002-0.07514986429080.56909321244712.30420884691.2709309045836.0800290371
107.814388553621.171540436711.931966129222.686949074480.3484040835952.205043281750.06356793091340.534683200081-0.319941970069-0.621950277315-0.2129201985640.233613923450.939060586311-0.2098257644050.4884782178120.651836239133-0.126719147675-0.01535030886710.540909761527-0.09678378440570.41682143486915.0727307489-4.8684300211132.7352196989
116.165434436470.07079399208811.027245486446.915965954240.2386533097916.310662508350.0733843926623-0.445726912914-0.3530001811030.171879186599-0.226798039202-0.1524282382490.762549819429-0.3581416484150.1373001998920.473924857112-0.0358594594025-0.004761771583360.2882556386570.02013285395830.33898299093618.7181362027-5.510158324142.4907889917
128.23865970252-0.9856010566930.2583493615486.08066920534-5.877742314426.04418018737-0.1365769156510.599771651867-0.0927597778785-1.516839966030.241401229438-0.3285611998631.339194793290.3761461437830.1245433726020.5349299040510.04926617602020.04510130809310.4172429688920.02070481337820.45316698307725.843581868-2.8640244718437.5955051646
133.51201535248-1.32469648354-0.906266117442.9331536006-0.2806530316269.62209502414-0.13954094097-0.2015625605370.3070749969650.196505652482-0.0469613923176-0.435360598710.04548349987680.2035065487580.08593443529920.352607372972-0.087563511978-0.1142491131980.392794104194-0.009834998691180.4113912327524.08160487336.3778786004839.5670206142
147.823731441622.79132088293.994067129139.645681254283.204371647823.05674629072-0.0653791938154-0.1174882693110.4880919001460.358471920891-0.1771350056670.422422799501-0.253837088963-1.234435217470.4758459908550.3889317969280.087135306804-0.05716563928620.496066471674-0.04185452197190.4343303403914.90158884928.4647383275636.7695910056
157.04241778346-5.084766471581.929131709533.74369161191-1.905405610334.739748262610.02474556889050.1345431701870.542636789952-0.5771594734620.0216083139969-0.6585617495090.697771221072-0.116112009509-0.2520017387920.627302202206-0.09644987043740.0003513168291470.320470176243-0.04379307327830.4302036520824.8506961083-3.2637428466332.7695209073
168.790448406170.598987717685.2050380872.73753357490.2938698290433.411273793140.274342587396-0.03483570052080.3469630344590.106328042843-0.1284818412531.355288515340.159015065745-1.37077656261-0.08065777037920.5421633389210.138215736843-0.08224084251380.4844438897320.06963744646040.71565980200917.349851773437.011101411640.8554342874
173.23085469551-0.435586058311-0.7985827544552.51657626977-2.942898012619.3951193098-0.6511425146520.4459285841140.2237415635420.3122221057470.02117602420870.730718112718-0.752629532727-0.5839278850540.7224256238870.9923889907220.0853043896128-0.01237540189630.431920352548-0.026005566020.5405180852317.517795625540.814181911144.7945713228
183.51627642218-1.02269996775-1.457107362099.899066110391.254082407586.895814143620.1372093434470.2331722359120.397375977114-0.583373530114-0.170972238649-0.405236183148-0.184437362446-0.2756623899220.1036709540130.8160338269790.0363815054204-0.02052396939210.361027578980.0994426455450.46630684570124.101839340644.857243860137.4242608622
193.97503388931-1.78234428181.005145270064.487536065921.223656839226.94582334542-0.119600148040.224575109971-0.380413580532-0.225653428533-0.06264293932920.1916357098420.16784339065-0.09832358803020.2048613429450.5918616693330.02318885166030.100645290810.3026173475690.04937311342330.34881932162825.742590688834.069686288339.7037783604
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 302 through 321 )AA302 - 3211 - 20
22chain 'A' and (resid 322 through 340 )AA322 - 34021 - 39
33chain 'A' and (resid 341 through 351 )AA341 - 35140 - 50
44chain 'A' and (resid 352 through 370 )AA352 - 37051 - 69
55chain 'B' and (resid 296 through 315 )BB296 - 3151 - 20
66chain 'B' and (resid 316 through 334 )BB316 - 33421 - 39
77chain 'B' and (resid 335 through 351 )BB335 - 35140 - 56
88chain 'B' and (resid 352 through 370 )BB352 - 37057 - 75
99chain 'C' and (resid 1 through 9 )CD1 - 91 - 9
1010chain 'C' and (resid 10 through 19 )CD10 - 1910 - 19
1111chain 'C' and (resid 20 through 42 )CD20 - 4220 - 42
1212chain 'C' and (resid 43 through 49 )CD43 - 4943 - 49
1313chain 'C' and (resid 50 through 60 )CD50 - 6050 - 60
1414chain 'C' and (resid 61 through 71 )CD61 - 7161 - 71
1515chain 'C' and (resid 72 through 77 )CD72 - 7772 - 77
1616chain 'D' and (resid 2 through 9 )DE2 - 91 - 8
1717chain 'D' and (resid 10 through 19 )DE10 - 199 - 18
1818chain 'D' and (resid 20 through 41 )DE20 - 4119 - 40
1919chain 'D' and (resid 42 through 76 )DE42 - 7641 - 75

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