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- PDB-8p14: USP28 USP domain in complex with Vismodegib -

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Basic information

Entry
Database: PDB / ID: 8p14
TitleUSP28 USP domain in complex with Vismodegib
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsONCOPROTEIN / Ubiquitin / Inhibitor / Deubiquitylase
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
Chem-VIS / Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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
CitationJournal: 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.
History
DepositionMay 11, 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.journal_abbrev ..._citation.country / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,5896
Polymers44,0261
Non-polymers5635
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-28 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.634, 106.634, 329.857
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 44026.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UCID oligomerization domain replaced by a linker,UCID oligomerization domain replaced by a linker
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-VIS / 2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide


Mass: 421.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14Cl2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M NaCl 0.1 M Li2SO4 0.1 M MES pH 6.4 14% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.57→47.97 Å / Num. obs: 44538 / % possible obs: 99.9 % / Redundancy: 19.1 % / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 2.57→2.68 Å / Num. unique obs: 2825 / CC1/2: 0.402

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H4I

6h4i


Resolution: 2.57→44.46 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 1982 4.45 %
Rwork0.1928 --
obs0.1939 44525 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 31 89 2806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052794
X-RAY DIFFRACTIONf_angle_d0.8113799
X-RAY DIFFRACTIONf_dihedral_angle_d13.3021012
X-RAY DIFFRACTIONf_chiral_restr0.051387
X-RAY DIFFRACTIONf_plane_restr0.009519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.630.36021420.3413009X-RAY DIFFRACTION100
2.63-2.710.33281400.32213024X-RAY DIFFRACTION100
2.71-2.790.33271450.3163069X-RAY DIFFRACTION100
2.79-2.880.37281430.31893031X-RAY DIFFRACTION100
2.88-2.980.34711390.27373046X-RAY DIFFRACTION100
2.98-3.10.23981450.23563025X-RAY DIFFRACTION100
3.1-3.240.23831400.21993060X-RAY DIFFRACTION100
3.24-3.410.20611420.18863031X-RAY DIFFRACTION100
3.41-3.620.22681350.19843045X-RAY DIFFRACTION100
3.62-3.90.24341410.17433040X-RAY DIFFRACTION100
3.9-4.290.22861390.15933040X-RAY DIFFRACTION100
4.29-4.910.16161460.14333030X-RAY DIFFRACTION100
4.92-6.190.19091480.17293043X-RAY DIFFRACTION100
6.19-44.460.18151370.18553050X-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)
14.5344-0.5318-0.13066.6538-0.01193.25140.13760.40860.6062-0.1375-0.0322-0.1517-0.7798-0.1633-0.13690.93970.0625-0.0510.61730.28360.786349.91944.834-38.0558
23.32361.1988-1.64643.08720.064.46680.1-0.33330.9740.5757-0.322-0.2805-0.69120.44150.23371.18990.0784-0.21530.55730.13340.988652.01515.3066-29.6756
31.9744-0.9498-1.67953.43581.4933.9349-0.0863-0.55920.37390.78190.0652-0.4282-0.10190.4325-0.02230.738-0.0003-0.11510.4934-0.08160.521754.2834-12.5623-12.4086
44.9026-0.1286-1.57675.00950.37326.31780.04650.52910.3258-0.0183-0.16210.1097-0.3142-0.23480.17260.5190.0547-0.11050.30920.02990.412849.4043-13.7782-30.1814
51.3673-0.04560.06793.4572-1.81483.8940.04960.72550.6037-0.31370.01090.3506-0.6614-0.3051-0.0950.77330.0541-0.07250.75240.17450.610248.0021-4.9814-40.19
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 227 )
2X-RAY DIFFRACTION2chain 'A' and (resid 228 through 293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 397 )
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 451 )
5X-RAY DIFFRACTION5chain 'A' and (resid 452 through 521 )

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