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- PDB-8p1q: USP28 in complex with FT206 -

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Basic information

Entry
Database: PDB / ID: 8p1q
TitleUSP28 in complex with FT206
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsONCOPROTEIN / USP28 / DUB / Ubiquitin / cancer
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: 2.79 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: To Be Published
Title: USP28 in complex with FT206
Authors: Sauer, F. / Karal Nair, R. / Kisker, C.
History
DepositionMay 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)116,8186
Polymers115,7662
Non-polymers1,0514
Water99155
1
A: Ubiquitin carboxyl-terminal hydrolase 28
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8186
Polymers115,7662
Non-polymers1,0514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554x+1/2,-y,-z-1/21
Buried area3040 Å2
ΔGint-23 kcal/mol
Surface area42560 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

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Components

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


Mass: 57883.141 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-WFT / 3-azanyl-N-[(2S)-6-[(1S,5R)-3,8-diazabicyclo[3.2.1]octan-3-yl]-1,2,3,4-tetrahydronaphthalen-2-yl]-6-methyl-thieno[2,3-b]pyridine-2-carboxamide


Mass: 447.596 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29N5OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 69.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.5 M Na-malonate, pH6.0 0.1M Na-citrate, pH 5.0

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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 PILATUS3 2M / Detector: PIXEL / Date: Apr 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.756→46.09 Å / Num. obs: 34993 / % possible obs: 94.6 % / Redundancy: 11.9 % / CC1/2: 0.998 / Net I/σ(I): 12.8
Reflection shellResolution: 2.756→3.042 Å / Num. unique obs: 2917 / CC1/2: 0.48

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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: 2.79→46.09 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 1216 3.51 %
Rwork0.2124 --
obs0.2132 34606 71.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 72 55 6761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026890
X-RAY DIFFRACTIONf_angle_d0.5279369
X-RAY DIFFRACTIONf_dihedral_angle_d13.0972491
X-RAY DIFFRACTIONf_chiral_restr0.041021
X-RAY DIFFRACTIONf_plane_restr0.0041242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.90.6702210.4657595X-RAY DIFFRACTION20
2.9-3.030.497620.37511759X-RAY DIFFRACTION34
3.03-3.190.3617860.30862518X-RAY DIFFRACTION49
3.19-3.390.29891180.27263308X-RAY DIFFRACTION65
3.39-3.650.33671650.27014390X-RAY DIFFRACTION86
3.65-4.020.24421870.21015110X-RAY DIFFRACTION100
4.02-4.60.20231920.17185164X-RAY DIFFRACTION100
4.6-5.80.18251910.18255193X-RAY DIFFRACTION100
5.8-100.2241940.21235353X-RAY DIFFRACTION99
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)
14.9688-2.5421-1.41244.12520.99953.0431-0.4066-1.57820.18090.65770.5114-0.1873-0.16440.74390.20760.35240.0202-0.05570.4952-0.07810.326226.9451-38.8628-24.4132
20.87410.8578-0.88421.9989-1.03541.3572-0.0294-0.00730.0049-0.5891-0.0005-0.1148-0.21260.12190.01150.7791-0.0634-0.00880.2631-0.04510.459835.484-24.492-55.7107
35.9963-1.6546-2.23452.46990.87393.374-0.3277-0.9421-0.19880.65090.17910.5459-0.1402-0.05940.12560.62330.04440.18620.3816-0.00590.6399.1678-36.5293-23.7612
41.9619-0.3623-0.81923.1198-1.79651.8668-0.21290.67680.2457-1.62050.5683-0.8231-0.63980.8735-0.07080.955-0.58841.51151.66040.0930.31568.458-41.7221-76.0691
54.65730.4567-1.31234.9747-0.16064.89130.04621.18170.6957-1.00330.36720.262-0.91660.0406-0.2330.453-0.11250.10680.74420.14470.5511-5.3912-39.9047-60.0945
6-0.47280.3538-0.47563.36141.71592.6645-0.29250.0181-0.02770.37170.3255-0.1366-0.39940.27520.23720.56350.1217-0.09490.4029-0.1070.7933-2.205-16.7443-27.5708
70.75010.2246-0.85451.2364-1.08042.9388-0.01970.74910.8396-1.03260.771-1.4658-1.04972.29240.02561.302-0.64140.77291.67410.05811.320712.3103-34.0198-65.7483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 398 )
2X-RAY DIFFRACTION2chain 'A' and (resid 399 through 625 )
3X-RAY DIFFRACTION3chain 'A' and (resid 626 through 701 )
4X-RAY DIFFRACTION4chain 'B' and (resid 151 through 225 )
5X-RAY DIFFRACTION5chain 'B' and (resid 226 through 398 )
6X-RAY DIFFRACTION6chain 'B' and (resid 399 through 594 )
7X-RAY DIFFRACTION7chain 'B' and (resid 595 through 690 )

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