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- PDB-8p1p: USP28 in complex with AZ1 -

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Basic information

Entry
Database: PDB / ID: 8p1p
TitleUSP28 in complex with AZ1
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsONCOPROTEIN / USP28 / Ubiquitin / inhibitor / AZ1
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 / cysteine-type deubiquitinase activity ...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 / cysteine-type deubiquitinase activity / cell population proliferation / Ub-specific processing proteases / nuclear body / DNA repair / DNA damage response / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Ubiquitin-specific protease UIM domain / : / UBA-like domain / : / 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 UIM domain / : / UBA-like domain / : / 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: 2.76 Å
AuthorsSauer, F. / Karal-Nair, R. / Kisker, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2243 Germany
German Research Foundation (DFG)KI562/8-2 Germany
Citation
Journal: Embo Rep. / Year: 2024
Title: Structural basis for the bi-specificity of USP25 and USP28 inhibitors.
Authors: Patzke, J.V. / Sauer, F. / Nair, R.K. / Endres, E. / Proschak, E. / Hernandez-Olmos, V. / Sotriffer, C. / Kisker, C.
#1: Journal: Mol Cell / Year: 2019
Title: Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities.
Authors: Sauer, F. / Klemm, T. / Kollampally, R.B. / Tessmer, I. / Nair, R.K. / Popov, N. / Kisker, C.
History
DepositionMay 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,8066
Polymers115,8482
Non-polymers9584
Water84747
1
A: Ubiquitin carboxyl-terminal hydrolase 28
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8066
Polymers115,8482
Non-polymers9584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554x+1/2,-y,-z-1/21
Buried area2970 Å2
ΔGint-38 kcal/mol
Surface area44390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.444, 105.541, 178.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (-0.937249275528, -0.0630279006468, -0.342915848661), (-0.00591682508518, 0.986258661315, -0.165102526214), (0.348609791463, -0.152713249987, -0.924743140864)Vector: 12. ...NCS oper: (Code: given
Matrix: (-0.937249275528, -0.0630279006468, -0.342915848661), (-0.00591682508518, 0.986258661315, -0.165102526214), (0.348609791463, -0.152713249987, -0.924743140864)
Vector: 12.867723959, -4.62369367591, -103.396185728)

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Components

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


Mass: 57924.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-WF0 / 2-[[5-bromanyl-2-[[4-fluoranyl-3-(trifluoromethyl)phenyl]methoxy]phenyl]methylamino]ethanol


Mass: 422.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16BrF4NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 M sodium malonate pH 6.0 0.1 M sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.76→48.35 Å / Num. obs: 34461 / % possible obs: 94.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 60.95 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.9
Reflection shellResolution: 2.76→3.008 Å / Num. unique obs: 1723 / CC1/2: 0.393

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→48.35 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 1213 3.52 %
Rwork0.2128 --
obs0.2138 34413 69.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7074 0 55 47 7176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037333
X-RAY DIFFRACTIONf_angle_d0.5589942
X-RAY DIFFRACTIONf_dihedral_angle_d14.272710
X-RAY DIFFRACTIONf_chiral_restr0.0391053
X-RAY DIFFRACTIONf_plane_restr0.0041308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.870.2526110.3459262X-RAY DIFFRACTION5
2.87-30.4367430.34271250X-RAY DIFFRACTION24
3-3.150.3787760.30972332X-RAY DIFFRACTION44
3.15-3.350.29781230.27563257X-RAY DIFFRACTION62
3.35-3.610.29851720.25164443X-RAY DIFFRACTION84
3.61-3.970.25151930.21425315X-RAY DIFFRACTION100
3.97-4.550.20661950.17175360X-RAY DIFFRACTION100
4.55-5.730.19141960.1765374X-RAY DIFFRACTION100
5.73-48.350.24032040.22125607X-RAY DIFFRACTION100
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)
12.9776-1.0029-0.13121.93350.05330.982-0.4317-1.744-0.32471.1510.64130.2127-0.4890.54710.22170.51740.2086-0.09660.8369-0.14060.179519.642-40.541-16.075
2-0.31421.4116-0.79721.1194-0.91250.50490.0341-0.15930.3765-0.6497-0.0916-0.0437-0.49790.1216-0.14930.745-0.04530.14640.13320.08250.468635.088-28.918-47.906
33.007-0.20820.56910.9217-0.15030.8319-0.2613-0.8857-0.45210.09280.37580.4290.0545-0.43320.17410.5777-0.08770.27040.42150.09580.62631.811-41.942-17.659
41.69030.3924-1.01582.229-0.12643.44920.02560.6330.1548-0.34820.2343-0.0145-0.72390.1443-0.11790.363-0.10170.05190.66120.01620.2949-1.771-39.75-65.906
5-0.37590.18210.10532.02811.11431.5662-0.22580.1550.14670.16850.13770.0446-0.5850.04390.21970.61280.1503-0.04170.3255-0.05380.5314-2.489-16.259-27.322
60.99880.1397-0.53521.2666-0.20541.61760.17960.84530.1579-0.61510.1973-0.6445-1.26411.28780.02770.8683-0.35490.25841.1653-0.09260.629512.303-34.486-69.712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 149:301 )A149 - 301
2X-RAY DIFFRACTION2( CHAIN A AND RESID 302:649 )A302 - 649
3X-RAY DIFFRACTION3( CHAIN A AND RESID 650:700 )A650 - 700
4X-RAY DIFFRACTION4( CHAIN B AND RESID 151:401 )B151 - 401
5X-RAY DIFFRACTION5( CHAIN B AND RESID 402:594 )B402 - 594
6X-RAY DIFFRACTION6( CHAIN B AND RESID 595:696 )B595 - 696

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