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- PDB-6heh: Structure of the catalytic domain of USP28 (insertion deleted) -

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Basic information

Entry
Database: PDB / ID: 6heh
TitleStructure of the catalytic domain of USP28 (insertion deleted)
ComponentsUbiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE / Ubiquitin / USP / Ubiquitin-specific protease / DUB / Deubiquitinase / protease / isopeptidase / USP28
Function / homology
Function and homology information


protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cell population proliferation ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cell population proliferation / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / DNA repair / DNA damage response / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / UBA-like superfamily / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsGersch, M. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council724804 United Kingdom
CitationJournal: Mol.Cell / Year: 2019
Title: Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity.
Authors: Gersch, M. / Wagstaff, J.L. / Toms, A.V. / Graves, B. / Freund, S.M.V. / Komander, D.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 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
Revision 1.3Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6843
Polymers44,5871
Non-polymers982
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomeric behavior observed by SAXS and SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-4 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.152, 189.152, 189.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-1028-

HOH

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28


Mass: 44586.691 Da / Num. of mol.: 1
Mutation: residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLacI / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 12% (w/v) PEG 8000, 100 mM sodium chloride, 200 mM lithium sulfate, 100 mM MES pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.26→50.55 Å / Num. obs: 27219 / % possible obs: 99.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Net I/σ(I): 19.8
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2698 / CC1/2: 0.827 / Rrim(I) all: 0.752 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HEI

6hei


Resolution: 2.26→50.55 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2161 1370 5.04 %
Rwork0.1956 --
obs0.1966 27199 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→50.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 5 128 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032815
X-RAY DIFFRACTIONf_angle_d0.63817
X-RAY DIFFRACTIONf_dihedral_angle_d23.221002
X-RAY DIFFRACTIONf_chiral_restr0.038396
X-RAY DIFFRACTIONf_plane_restr0.004496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2605-2.34130.27151260.25232555X-RAY DIFFRACTION99
2.3413-2.4350.25541200.23182530X-RAY DIFFRACTION100
2.435-2.54580.2691240.23162569X-RAY DIFFRACTION100
2.5458-2.680.27681380.22842552X-RAY DIFFRACTION100
2.68-2.84790.24591160.22312549X-RAY DIFFRACTION100
2.8479-3.06780.21721490.21262564X-RAY DIFFRACTION100
3.0678-3.37650.21151440.20832567X-RAY DIFFRACTION100
3.3765-3.86490.22721570.17862572X-RAY DIFFRACTION100
3.8649-4.86870.18311440.15542627X-RAY DIFFRACTION100
4.8687-50.56560.19921520.19992744X-RAY DIFFRACTION99

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