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- PDB-6cga: Structure of the PR-DUB complex -

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Basic information

Entry
Database: PDB / ID: 6cga
TitleStructure of the PR-DUB complex
Components
  • Polycomb protein Asx
  • Ubiquitin carboxyl-terminal hydrolase calypso
KeywordsHYDROLASE / DUB complex / nucleosome binding protein / hetero-tetramer
Function / homology
Function and homology information


antennal development / apposition of dorsal and ventral imaginal disc-derived wing surfaces / PR-DUB complex / specification of segmental identity, abdomen / sex comb development / syncytial blastoderm mitotic cell cycle / UCH proteinases / cell fate determination / deubiquitinase activator activity / anterior/posterior axis specification ...antennal development / apposition of dorsal and ventral imaginal disc-derived wing surfaces / PR-DUB complex / specification of segmental identity, abdomen / sex comb development / syncytial blastoderm mitotic cell cycle / UCH proteinases / cell fate determination / deubiquitinase activator activity / anterior/posterior axis specification / protein deubiquitination / epigenetic regulation of gene expression / animal organ morphogenesis / heterochromatin formation / ubiquitin-dependent protein catabolic process / regulation of gene expression / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily ...Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase calypso / Polycomb group protein Asx
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFoglizzo, M. / Middleton, A.J. / Day, C.L. / Mace, P.D.
CitationJournal: Nat Commun / Year: 2018
Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes.
Authors: Foglizzo, M. / Middleton, A.J. / Burgess, A.E. / Crowther, J.M. / Dobson, R.C.J. / Murphy, J.M. / Day, C.L. / Mace, P.D.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ubiquitin carboxyl-terminal hydrolase calypso
B: Polycomb protein Asx
C: Ubiquitin carboxyl-terminal hydrolase calypso
D: Polycomb protein Asx


Theoretical massNumber of molelcules
Total (without water)112,6194
Polymers112,6194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, cross-linking, equilibrium centrifugation, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.170, 65.630, 162.760
Angle α, β, γ (deg.)90.000, 114.350, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 46 through 93 or resid 110...
21(chain C and (resid 46 through 159 or resid 161...
12chain B
22(chain D and (resid 214 through 253 or resid 275 through 309))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TRPTRPILEILE(chain A and (resid 46 through 93 or resid 110...AA46 - 937 - 54
121PHEPHELYSLYS(chain A and (resid 46 through 93 or resid 110...AA110 - 11271 - 73
131ALAALATHRTHR(chain A and (resid 46 through 93 or resid 110...AA116 - 15977 - 120
141THRTHRSERSER(chain A and (resid 46 through 93 or resid 110...AA161 - 243122 - 204
151TRPTRPARGARG(chain A and (resid 46 through 93 or resid 110...AA246 - 257207 - 218
161ASPASPSERSER(chain A and (resid 46 through 93 or resid 110...AA266 - 398227 - 359
211TRPTRPTHRTHR(chain C and (resid 46 through 159 or resid 161...CC46 - 1597 - 120
221THRTHRARGARG(chain C and (resid 46 through 159 or resid 161...CC161 - 194122 - 155
231ALAALAARGARG(chain C and (resid 46 through 159 or resid 161...CC211 - 257172 - 218
241ASPASPLEULEU(chain C and (resid 46 through 159 or resid 161...CC266 - 303227 - 264
251ARGARGSERSER(chain C and (resid 46 through 159 or resid 161...CC335 - 398296 - 359
112THRTHRLYSLYSchain BBB214 - 3098 - 103
212THRTHRARGARG(chain D and (resid 214 through 253 or resid 275 through 309))DD214 - 2538 - 47
222ARGARGLYSLYS(chain D and (resid 214 through 253 or resid 275 through 309))DD275 - 30969 - 103

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase calypso / BAP1 homolog


Mass: 41081.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: calypso, CG8445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7K5N4, ubiquitinyl hydrolase 1
#2: Protein Polycomb protein Asx / Additional sex combs


Mass: 15228.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Asx, CG8787 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V727

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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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.5
Details: 0.1 M Bis-Tris propane pH 8.5, 0.05 M potassium iodide, 13% (w/v) PEG 3350 and 10% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.5→43.672 Å / Num. obs: 18300 / % possible obs: 98.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 112.87 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.1
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4333 / CC1/2: 0.613 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UEM

4uem


Resolution: 3.5→43.672 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.56
RfactorNum. reflection% reflection
Rfree0.294 730 4.74 %
Rwork0.2442 --
obs0.2465 15404 83.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 295.88 Å2 / Biso mean: 132.2666 Å2 / Biso min: 36.5 Å2
Refinement stepCycle: final / Resolution: 3.5→43.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 0 0 0 5875
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026001
X-RAY DIFFRACTIONf_angle_d0.5578101
X-RAY DIFFRACTIONf_chiral_restr0.039902
X-RAY DIFFRACTIONf_plane_restr0.0041050
X-RAY DIFFRACTIONf_dihedral_angle_d2.2084218
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2492X-RAY DIFFRACTION11.348TORSIONAL
12C2492X-RAY DIFFRACTION11.348TORSIONAL
21B656X-RAY DIFFRACTION11.348TORSIONAL
22D656X-RAY DIFFRACTION11.348TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5003-3.77040.2969740.26281415148941
3.7704-4.14950.34521450.26192748289379
4.1495-4.74940.3141740.23493477365199
4.7494-5.98120.2871640.27113502366699
5.9812-43.6750.27151730.22863532370597
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)
16.32381.5988-0.02986.34830.08926.23540.204-0.6537-0.22620.36710.24530.16830.32530.2396-0.36940.510.0029-0.21120.50930.10340.43162.9342-48.854418.3261
21.1502-0.2071-0.77970.057-0.04090.5171-0.3621-0.3640.6940.78960.747-0.386-0.280.1039-0.20310.67350.0357-0.04380.6472-0.17050.84047.2743-28.625431.8936
37.8848-3.94085.1054.5659-5.97787.9007-0.48340.0577-0.5225-1.43070.3515-0.74061.871-1.29950.08110.9487-0.41020.2651.3279-0.07350.840740.3377-32.675427.1401
47.02-0.44661.34458.1693-2.33514.9112-0.57960.34940.11270.42870.4279-0.10560.2348-0.89150.06360.4418-0.26510.19910.8038-0.28160.910531.2773-27.987223.2111
59.28273.05161.24944.98483.30974.68310.9288-0.11231.1992-0.05590.1839-0.1973-3.62743.5062-1.24322.63040.43410.43931.9755-0.35041.360441.6954-42.20499.6584
69.4909-0.8652-0.21546.38041.63776.89760.0182-0.14450.50991.1187-0.85330.28080.94060.18410.81471.11570.1057-0.02240.53840.02230.9953-3.5342-40.587569.8783
72.5516-1.03812.76281.32380.53646.3182-0.7945-0.47342.16390.8258-0.43140.7282-0.7605-1.08870.95721.81870.23650.01521.0797-0.17111.8743-10.006-28.030777.7611
87.65142.0842-0.02837.25820.45443.1954-0.3526-0.90210.72850.52220.6353-0.6065-1.4750.0933-0.18431.4797-0.0878-0.16980.8003-0.18520.68890.4868-38.921773.4428
90.70450.00370.32760.3705-0.92011.757-0.13590.5128-0.17370.4222-0.1624-0.1807-0.3860.04640.32830.9460.19920.0170.6239-0.02540.986-17.7564-44.455153.8424
105.60271.6752-1.2494.7753-0.71523.2725-0.0513-1.6335-1.13790.1287-0.109-1.3420.381.85531.13180.76580.35330.39782.14880.79841.3435-16.4047-77.515869.6329
117.86670.16644.69463.2376-3.11956.001-0.65572.338-0.4263-1.9178-0.0671-1.1570.26831.06520.4681.8102-0.60711.05711.2727-0.36161.5389-29.472-72.747860.1002
120.4024-0.2946-0.23530.22140.25190.79070.0903-0.0745-0.09130.1218-0.17760.3287-0.0634-1.14880.14431.1371-0.09651.3091.4337-0.33092.065-34.3358-67.253168.2767
135.27462.04831.19343.08090.35870.28540.34360.521.9614-0.39220.5165-0.448-1.7421-0.5853-0.22141.09430.0671-0.03790.79430.02622.0468-30.0651-59.375362.8139
147.4123-0.2827-2.59163.3788-1.62255.6397-0.2697-0.9229-0.04630.0309-0.0369-0.82240.17980.7520.760.7006-0.12791.03551.08280.51382.1589-14.0711-68.354171.1959
151.91290.5376-0.23250.4855-0.26140.8139-0.5996-1.0443-0.0332-0.38730.6670.39270.1984-0.59660.1670.94920.0316-0.03142.99820.64240.8367-15.7008-70.848191.2553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 253 )A44 - 253
2X-RAY DIFFRACTION2chain 'A' and (resid 254 through 398 )A254 - 398
3X-RAY DIFFRACTION3chain 'B' and (resid 214 through 233 )B214 - 233
4X-RAY DIFFRACTION4chain 'B' and (resid 234 through 298 )B234 - 298
5X-RAY DIFFRACTION5chain 'B' and (resid 299 through 309 )B299 - 309
6X-RAY DIFFRACTION6chain 'C' and (resid 46 through 140 )C46 - 140
7X-RAY DIFFRACTION7chain 'C' and (resid 141 through 165 )C141 - 165
8X-RAY DIFFRACTION8chain 'C' and (resid 166 through 253 )C166 - 253
9X-RAY DIFFRACTION9chain 'C' and (resid 254 through 399 )C254 - 399
10X-RAY DIFFRACTION10chain 'D' and (resid 214 through 229 )D214 - 229
11X-RAY DIFFRACTION11chain 'D' and (resid 230 through 237 )D230 - 237
12X-RAY DIFFRACTION12chain 'D' and (resid 238 through 247 )D238 - 247
13X-RAY DIFFRACTION13chain 'D' and (resid 248 through 277 )D248 - 277
14X-RAY DIFFRACTION14chain 'D' and (resid 278 through 303 )D278 - 303
15X-RAY DIFFRACTION15chain 'D' and (resid 304 through 309 )D304 - 309

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