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- PDB-2len: Solution structure of UCHL1 S18Y variant -

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Basic information

Entry
Database: PDB / ID: 2len
TitleSolution structure of UCHL1 S18Y variant
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L1
KeywordsHYDROLASE
Function / homology
Function and homology information


axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination ...axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination / regulation of macroautophagy / negative regulation of MAP kinase activity / axon cytoplasm / positive regulation of glycolytic process / ubiquitin binding / response to ischemia / UCH proteinases / cellular response to xenobiotic stimulus / omega peptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / neuronal cell body / ubiquitin protein ligase binding / endoplasmic reticulum membrane / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase isozyme L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsTse, H.
CitationJournal: to be published
Title: Backbone and side-chain (1)H, (15)N and (13)C resonance assignments of S18Y mutant of ubiquitin carboxy-terminal hydrolase L1
Authors: Tse, H. / Sze, K. / Hu, H.
History
DepositionJun 19, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1


Theoretical massNumber of molelcules
Total (without water)26,0031
Polymers26,0031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L1 / UCH-L1 / Neuron cytoplasmic protein 9.5 / PGP 9.5 / PGP9.5 / Ubiquitin thioesterase L1


Mass: 26002.594 Da / Num. of mol.: 1 / Mutation: S18Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 / References: UniProt: P09936, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D HN(CA)CO
11113D (H)CCH-COSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic
11513D 1H-15N TOCSY

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Sample preparation

DetailsContents: 0.7-0.8mM [U-99% 13C; U-99% 15N] UCHL1 S18Y variant-1, 20mM sodium phosphate-2, 100mM sodium chloride-3, 3mM DTT-4, 90% H2O-5, 10% D2O-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMUCHL1 S18Y variant-1[U-99% 13C; U-99% 15N]0.7-0.81
20 mMsodium phosphate-21
100 mMsodium chloride-31
3 mMDTT-41
90 %H2O-51
10 %D2O-61
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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