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- PDB-6hgc: Structure of Calypso in complex with DEUBAD of ASX -

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Basic information

Entry
Database: PDB / ID: 6hgc
TitleStructure of Calypso in complex with DEUBAD of ASX
Components
  • (Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso) x 2
  • Polycomb protein Asx
KeywordsHYDROLASE / Deubiquitinase / Polycomb group proteins / transcription / gene repression
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 ...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 / heterochromatin formation / animal organ morphogenesis / chromatin organization / 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 / 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. ...Polycomb protein ASX / 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 protein Asx
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.02 Å
AuthorsDe, I. / Chittock, E.C. / Groetsch, H. / Miller, T.C.R. / McCarthy, A.A. / Mueller, C.W.
Funding support1items
OrganizationGrant numberCountry
European Commission277899
CitationJournal: Structure / Year: 2019
Title: Structural Basis for the Activation of the Deubiquitinase Calypso by the Polycomb Protein ASX.
Authors: De, I. / Chittock, E.C. / Grotsch, H. / Miller, T.C.R. / McCarthy, A.A. / Muller, C.W.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso
C: Polycomb protein Asx
B: Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso


Theoretical massNumber of molelcules
Total (without water)85,8083
Polymers85,8083
Non-polymers00
Water00
1
A: Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso
C: Polycomb protein Asx


Theoretical massNumber of molelcules
Total (without water)50,8242
Polymers50,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-30 kcal/mol
Surface area22520 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso


Theoretical massNumber of molelcules
Total (without water)34,9851
Polymers34,9851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.505, 119.505, 408.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 38469.738 Da / Num. of mol.: 1
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: 12353.792 Da / Num. of mol.: 1
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
#3: Protein Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso / BAP1 homolog


Mass: 34984.723 Da / Num. of mol.: 1
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

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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: 4.92 Å3/Da / Density % sol: 75.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 6% PEG MME 5K, 0.1 M HEPES pH 7.0, 5 % Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9747 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 3.02→103.49 Å / Num. obs: 31261 / % possible obs: 89.3 % / Redundancy: 18.5 % / Net I/σ(I): 13.3
Reflection shellResolution: 3.02→3.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 3.02→72.729 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.32
RfactorNum. reflection% reflection
Rfree0.2917 1997 6.4 %
Rwork0.268 --
obs0.2695 31225 89.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.56 Å2 / Biso mean: 72.8074 Å2 / Biso min: 13.95 Å2
Refinement stepCycle: final / Resolution: 3.02→72.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 0 0 5185
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035307
X-RAY DIFFRACTIONf_angle_d0.5657161
X-RAY DIFFRACTIONf_chiral_restr0.038802
X-RAY DIFFRACTIONf_plane_restr0.004930
X-RAY DIFFRACTIONf_dihedral_angle_d15.6473223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0201-3.09560.3071720.32381053112546
3.0956-3.17930.3468830.34131216129953
3.1793-3.27280.38311010.33371486158765
3.2728-3.37850.36391280.32291863199181
3.3785-3.49920.32981550.32032274242999
3.4992-3.63930.34621580.308423082466100
3.6393-3.80490.30951570.288922942451100
3.8049-4.00550.32871590.264723162475100
4.0055-4.25650.32291590.238923242483100
4.2565-4.58510.21061600.218823512511100
4.5851-5.04640.24791600.216923422502100
5.0464-5.77630.28781630.254223792542100
5.7763-7.27650.31181660.279724232589100
7.2765-72.74970.26251760.27552599277599

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