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- PDB-7yv4: Crystal structure of human UCHL3 in complex with Farrerol -

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Basic information

Entry
Database: PDB / ID: 7yv4
TitleCrystal structure of human UCHL3 in complex with Farrerol
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L3
KeywordsHYDROLASE / Activator / Complex / Ubiquitinase
Function / homology
Function and homology information


deNEDDylase activity / protein deubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / post-translational protein modification / ubiquitin binding / protein catabolic process / UCH proteinases / Neddylation / peptidase activity / ubiquitin-dependent protein catabolic process ...deNEDDylase activity / protein deubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / post-translational protein modification / ubiquitin binding / protein catabolic process / UCH proteinases / Neddylation / peptidase activity / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein ubiquitination / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-JXY / Ubiquitin carboxyl-terminal hydrolase isozyme L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMao, Z.Y. / Xu, X.J. / Zhang, W.T.
Funding support China, 8items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82071565 China
National Natural Science Foundation of China (NSFC)81972457 China
National Natural Science Foundation of China (NSFC)32171288 China
National Natural Science Foundation of China (NSFC)81973500 China
National Natural Science Foundation of China (NSFC)31721003 China
National Natural Science Foundation of China (NSFC)31820103009 China
National Natural Science Foundation of China (NSFC)31871446 China
National Natural Science Foundation of China (NSFC)32070857 China
CitationJournal: Nat Commun / Year: 2023
Title: Farrerol directly activates the deubiqutinase UCHL3 to promote DNA repair and reprogramming when mediated by somatic cell nuclear transfer.
Authors: Zhang, W. / Wang, M. / Song, Z. / Fu, Q. / Chen, J. / Zhang, W. / Gao, S. / Sun, X. / Yang, G. / Zhang, Q. / Yang, J. / Tang, H. / Wang, H. / Kou, X. / Wang, H. / Mao, Z. / Xu, X. / Gao, S. / Jiang, Y.
History
DepositionAug 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5142
Polymers26,2141
Non-polymers3001
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.054, 63.873, 77.161
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L3 / UCH-L3 / Ubiquitin thioesterase L3


Mass: 26213.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL3 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P15374, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-JXY / (2~{S})-2-(4-hydroxyphenyl)-6,8-dimethyl-5,7-bis(oxidanyl)-2,3-dihydrochromen-4-one / Farrerol


Mass: 300.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 1.4M Sodium Citrate tribasic dihydrate, 0.1M HEPES Sodium pH 7.0
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.58→24.6 Å / Num. obs: 32507 / % possible obs: 96.76 % / Redundancy: 12.5 % / Biso Wilson estimate: 20.04 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 20.67
Reflection shellResolution: 1.58→1.63 Å / Rmerge(I) obs: 0.158 / Num. unique obs: 32507

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ISU

6isu


Resolution: 1.58→24.6 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1999 6.15 %
Rwork0.1789 30508 -
obs0.1806 32507 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.55 Å2 / Biso mean: 27.1534 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.58→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 38 261 1922
Biso mean--23.83 35.56 -
Num. residues----202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.620.30671370.28952081221896
1.62-1.660.3021380.255221102248100
1.66-1.710.26661420.21521592301100
1.71-1.770.2511410.208521652306100
1.77-1.830.21721400.191521492289100
1.83-1.90.21961410.188421612302100
1.9-1.990.25461440.191521832327100
1.99-2.090.2411410.178421632304100
2.09-2.230.19761440.171721782322100
2.23-2.40.18951420.166821772319100
2.4-2.640.2041450.177222102355100
2.64-3.020.20241430.191221932336100
3.02-3.80.18971470.163422442391100
3.8-24.60.1821540.163923352489100
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)
17.35271.4684-0.4984.13830.44183.80010.1076-0.7691-0.38180.4734-0.0239-0.27440.42380.26230.00290.28010.0452-0.05880.22830.03590.2349-7.9267-7.282.0215
22.7992-0.1689-0.02841.36950.28582.0957-0.072-0.1507-0.02520.09380.1002-0.0256-0.00070.1368-0.0380.1312-0.0081-0.01850.13170.02870.1312-10.57885.27855.0889
33.3756-0.99581.53346.7882-5.3058.9880.0335-0.1532-0.2538-0.24130.0150.36940.2622-0.4359-0.03130.1372-0.01560.00760.194-0.05510.2334-34.72933.6698-5.5874
44.0948-0.92991.24371.48480.28842.79970.03230.2521-0.13460.0240.03830.10360.07040.0369-0.04860.15660.00240.0150.173-0.03730.1388-16.15020.71-9.7661
53.42331.19361.10672.12131.46353.1069-0.00830.3883-0.2296-0.05190.1677-0.32570.17680.6795-0.16880.18880.01740.03330.2989-0.06730.1898-4.9922-2.8159-14.7728
65.3801-2.96772.22527.3399-1.89956.23320.0510.7231-0.828-0.3016-0.20250.23950.5608-0.5710.05280.244-0.04850.03970.3215-0.12720.2215-17.2262-8.759-16.5664
72.9129-0.25280.04041.46840.96342.45-0.04650.0652-0.09290.00330.01870.03480.05270.02440.06070.1452-0.0026-0.00740.11520.00520.1134-19.35786.2311-3.1974
82.2792-1.20581.32331.8920.69912.3221-0.0077-0.5704-0.5130.33060.03670.10280.1706-0.20460.0190.2521-0.03090.030.21090.04010.1505-17.1323.14987.7698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 22 )A6 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 59 )A23 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 76 )A60 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 110 )A77 - 110
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 130 )A111 - 130
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 140 )A131 - 140
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 215 )A141 - 215
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 230 )A216 - 230

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