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- PDB-8itn: Crystal structure of USP47apo catalytic domain -

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Basic information

Entry
Database: PDB / ID: 8itn
TitleCrystal structure of USP47apo catalytic domain
ComponentsUbiquitin carboxyl-terminal hydrolase 47
KeywordsHYDROLASE / inhibitor / ubiquitin specific protease
Function / homology
Function and homology information


anterior/posterior axis specification, embryo / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 47, C-terminal / Ubiquitin carboxyl-terminal hydrolase 47 C-terminal / 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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 47
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKim, E.E. / Shin, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Commun Biol / Year: 2023
Title: Structural and functional characterization of USP47 reveals a hot spot for inhibitor design.
Authors: Shin, S.C. / Park, J. / Kim, K.H. / Yoon, J.M. / Cho, J. / Ha, B.H. / Oh, Y. / Choo, H. / Song, E.J. / Kim, E.E.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 47
B: Ubiquitin carboxyl-terminal hydrolase 47
C: Ubiquitin carboxyl-terminal hydrolase 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,8835
Polymers172,7523
Non-polymers1312
Water1,874104
1
A: Ubiquitin carboxyl-terminal hydrolase 47
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2994
Polymers115,1682
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4420 Å2
ΔGint-21 kcal/mol
Surface area31980 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 47
C: Ubiquitin carboxyl-terminal hydrolase 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2333
Polymers115,1682
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-13 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.077, 58.908, 251.932
Angle α, β, γ (deg.)90.00, 96.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 47 / Ubiquitin thioesterase 47 / Ubiquitin-specific-processing protease 47


Mass: 57583.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_T05H10.1, T05H10.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q22240, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M imidazole-malate (pH 5.5) and 18% (v/v) PEG 4000
PH range: 4.5 - 6.0

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: 298 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 41388 / % possible obs: 93.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.073 / Χ2: 0.848 / Net I/σ(I): 9.4 / Num. measured all: 223996
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.6-2.692.20.29175840.385190.1
2.69-2.82.30.25276960.428192.1
2.8-2.932.50.2178300.466193.8
2.93-3.082.70.16778800.549195.1
3.08-3.282.90.13780640.644196.8
3.28-3.533.10.10180860.848198.1
3.53-3.882.90.10160391.316172.7
3.88-4.453.10.07779991.38196.5
4.45-5.63.40.05983001.056199
5.6-6.53.60.03282500.917199.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.20.1-4487refinement
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→35.5 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 2080 5.03 %
Rwork0.258 --
obs0.2586 41388 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 2 104 8432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.503
X-RAY DIFFRACTIONf_dihedral_angle_d11.1133135
X-RAY DIFFRACTIONf_chiral_restr0.0371236
X-RAY DIFFRACTIONf_plane_restr0.0041499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.30841360.30842568X-RAY DIFFRACTION93
2.65-2.720.28821350.2882598X-RAY DIFFRACTION98
2.72-2.790.3141480.30492679X-RAY DIFFRACTION98
2.79-2.870.33431260.31922615X-RAY DIFFRACTION98
2.87-2.970.32261470.28912679X-RAY DIFFRACTION98
2.97-3.070.29861340.29322709X-RAY DIFFRACTION99
3.07-3.20.29721500.28752633X-RAY DIFFRACTION99
3.2-3.340.33611700.29642675X-RAY DIFFRACTION99
3.34-3.520.26171260.26172726X-RAY DIFFRACTION99
3.52-3.740.3118820.31181746X-RAY DIFFRACTION64
3.74-4.020.30251390.25252634X-RAY DIFFRACTION97
4.03-4.430.22421520.22422713X-RAY DIFFRACTION100
4.43-5.070.23031350.1992769X-RAY DIFFRACTION100
5.07-6.380.2351420.23372732X-RAY DIFFRACTION99
6.38-7.50.22721580.21332832X-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)
11.80490.5379-0.7271.2339-1.23192.81090.07070.80630.8488-0.3983-0.2789-0.6450.3250.455-0.29960.31390.11710.18710.45870.33680.6147-2.2289.038799.9266
21.29450.16030.224.053-0.56652.39910.04370.34610.9625-0.0438-0.1284-0.0111-0.45360.0581-0.57630.42610.017-0.01570.32680.42110.8765-14.353216.331598.5514
31.9066-0.1491-0.00632.06230.08071.59840.12420.30231.0307-0.0929-0.07020.152-0.11050.0870.01750.3830.09020.0740.32170.150.7029-16.014112.7911107.6635
43.04120.8576-0.33361.4591-0.84560.76080.06040.4282-0.1311-0.0968-0.0188-0.0610.0642-0.0391-0.00870.21260.0679-0.04140.119-0.06730.3454-16.8143-9.7274112.2286
51.5697-0.39910.03852.3383-1.26973.145-0.0172-0.220.18360.0107-0.3328-0.62370.15720.4840.21990.22830.0250.02860.2650.03730.3978-0.0467-4.2913108.1703
62.5238-1.41630.14910.8956-0.56243.79930.0906-0.18420.1204-0.6352-0.1238-0.0382-0.6529-0.40530.19230.67460.2112-0.03110.4322-0.02860.4024-16.08716.487787.897
71.98490.8815-0.58822.93330.1431.6038-0.16110.5963-0.17930.26890.4136-0.5090.3570.6731-0.14950.7148-0.0536-0.04261.8295-0.22530.53358.14583.342622.4561
82.2382-0.1694-0.99431.31971.07062.496-0.06610.54820.1167-0.00150.22840.1440.13470.09740.01550.6651-0.1891-0.01331.4527-0.02560.3762-7.78556.576122.325
92.77940.0517-0.87713.5446-0.55293.92810.21440.4942-0.22220.23250.2145-0.42930.43640.7783-0.33461.41320.3697-0.11721.1307-0.11060.53185.9341-3.015165.8648
100.69120.2544-0.16541.01750.40.4043-0.06090.7505-0.74220.91770.23190.00340.41980.109-0.3011.4599-0.09090.06710.9687-0.10350.7104-18.366-10.09853.1304
111.4365-0.22260.7370.77860.41512.5207-0.1420.3409-0.00940.33540.13650.06630.20520.21250.04611.0369-0.07360.15230.7895-0.0270.4037-11.19717.168158.5793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 76 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 152 )
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 437 )
5X-RAY DIFFRACTION5chain 'A' and (resid 438 through 474 )
6X-RAY DIFFRACTION6chain 'A' and (resid 475 through 492 )
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 231 )
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 492 )
9X-RAY DIFFRACTION9chain 'C' and (resid 76 through 194 )
10X-RAY DIFFRACTION10chain 'C' and (resid 195 through 231 )
11X-RAY DIFFRACTION11chain 'C' and (resid 232 through 492 )

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