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- PDB-7tuo: Crystal structure analysis of human USP28 complex with a compound -

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Basic information

Entry
Database: PDB / ID: 7tuo
TitleCrystal structure analysis of human USP28 complex with a compound
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE/HYDROLASE INHIBITOR / deubiquitinase / inhibitor / protein-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-KL9 / Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of human USP28 complex with a compound
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8514
Polymers44,9721
Non-polymers8793
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.640, 114.640, 114.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1081-

HOH

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Components

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


Mass: 44972.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-KL9 / 7-amino-N-(2-{4-[(1R,3s,5S)-8-azabicyclo[3.2.1]octan-3-yl]phenyl}ethyl)-3-methylthieno[2,3-b]pyrazine-6-carboxamide


Mass: 421.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N5OS / Feature type: SUBJECT OF INVESTIGATION
#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.: 205 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4M Sodium maleic acid, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.96→81.06 Å / Num. obs: 36300 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 36.62 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.112 / Net I/σ(I): 17.3 / Num. measured all: 496809
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.96-1.99141.42500517920.5942.22499.9
5.32-81.1312.555.52419719420.010.035100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HEH

6heh


Resolution: 1.96→81.06 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 1824 5.03 %
Rwork0.1777 34445 -
obs0.1791 36269 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.13 Å2 / Biso mean: 47.6014 Å2 / Biso min: 19.6 Å2
Refinement stepCycle: final / Resolution: 1.96→81.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 115 205 2950
Biso mean--61.38 48.25 -
Num. residues----320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.96-2.010.34631410.309226222763
2.01-2.070.27811330.247926262759
2.07-2.140.24731330.224326242757
2.14-2.220.27351520.199426032755
2.22-2.30.20991120.207926462758
2.3-2.410.25971380.207626332771
2.41-2.540.23341250.222126572782
2.54-2.690.25631220.198126552777
2.7-2.90.23031390.18426472786
2.9-3.190.23191780.188726142792
3.2-3.650.19611290.147426762805
3.66-4.610.15811700.142726682838
4.61-81.060.16921520.168627742926
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)
12.05891.0571-0.27032.31870.02661.1883-0.00980.13140.3267-0.1960.04020.2159-0.2206-0.1025-0.00010.29980.05860.01240.34050.06550.37488.540729.6779-15.6589
20.3877-0.0466-0.42670.2363-0.08770.5524-0.07530.2608-0.09840.08030.05830.2910.2451-0.50320.00020.3647-0.065-0.00160.45760.01960.3448-1.02369.2733-17.752
31.0410.7802-0.5322.1248-0.73051.95880.02230.2476-0.0545-0.02560.04550.56360.0424-0.57480.00760.31480.0173-0.03140.41510.0280.3491-3.18559.6094-10.1027
41.6391.69150.66412.1844-0.08242.24070.0922-0.20370.33190.2147-0.03480.053-0.23380.07160.00110.28010.00330.02370.30150.01880.293310.452821.6193-3.2172
50.60990.509-0.14270.77-0.46930.40350.0226-0.10660.09150.0852-0.0285-0.0723-0.15820.17670.0010.32670.01060.01230.35070.02230.364512.468118.1124-8.9695
61.2403-0.2106-0.14821.0437-0.59460.88860.3664-0.45890.69780.23250.09590.1153-0.9787-0.2670.00110.4924-0.04730.08530.513-0.07610.620625.373845.5454-4.7575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 325 )A149 - 325
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 368 )A326 - 368
3X-RAY DIFFRACTION3chain 'A' and (resid 369 through 582 )A369 - 582
4X-RAY DIFFRACTION4chain 'A' and (resid 583 through 625 )A583 - 625
5X-RAY DIFFRACTION5chain 'A' and (resid 626 through 674 )A626 - 674
6X-RAY DIFFRACTION6chain 'A' and (resid 675 through 699 )A675 - 699

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