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- PDB-2klc: NMR solution structure of human ubiquitin-like domain of ubiquili... -

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Basic information

Entry
Database: PDB / ID: 2klc
TitleNMR solution structure of human ubiquitin-like domain of ubiquilin 1, Northeast Structural Genomics Consortium (NESG) target HT5A
ComponentsUbiquilin-1
KeywordsStructural Genomics / Unknown function / ubiquitin-like / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Structural Genomics Consortium / SGC / protein binding / UBL / Ontario Centre for Structural Proteomics / OCSP / proteasome / ubiquitin ligase-associated / ubiquitination / protein degradation / Alzheimer's / Nucleus / Phosphoprotein / Ontario Centre for Structural Proteomics (OCSP)
Function / homology
Function and homology information


negative regulation of store-operated calcium channel activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of ERAD pathway / aggrephagy / regulation of proteasomal ubiquitin-dependent protein catabolic process / aggresome / regulation of protein ubiquitination / autophagosome maturation / autophagosome assembly ...negative regulation of store-operated calcium channel activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of ERAD pathway / aggrephagy / regulation of proteasomal ubiquitin-dependent protein catabolic process / aggresome / regulation of protein ubiquitination / autophagosome maturation / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / regulation of macroautophagy / ERAD pathway / response to endoplasmic reticulum stress / proteasome complex / positive regulation of protein ubiquitination / macroautophagy / kinase binding / Cargo recognition for clathrin-mediated endocytosis / cellular response to hypoxia / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsDoherty, R.S. / Dhe-Paganon, S. / Fares, C. / Lemak, S. / Gutmanas, A. / Garcia, M. / Yee, A. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) ...Doherty, R.S. / Dhe-Paganon, S. / Fares, C. / Lemak, S. / Gutmanas, A. / Garcia, M. / Yee, A. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution structure of ubiquitin-like domain of ubiquilin 1
Authors: Doherty, R.S. / Dhe-Paganon, S. / Fares, C. / Lemak, S. / Gutmanas, A. / Garcia, M. / Yee, A. / Montelione, G.T. / Arrowsmith, C.H.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionJun 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquilin-1


Theoretical massNumber of molelcules
Total (without water)11,6231
Polymers11,6231
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 #1lowest energy

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Components

#1: Protein Ubiquilin-1 / Protein linking IAP with cytoskeleton 1 / PLIC-1 / hPLIC-1


Mass: 11623.194 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain: Residues 34-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DA41, PLIC1, UBQLN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UMX0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D (H)CCH-TOCSY
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D 1H-13C arom NOESY
1912D 1H-15 HSQC (IPAP)
11012D 1H-15N HSQC
11112D 1H-13C Constant Time HSQC
11213D HBHA(CO)NH
11313D HNCO (IPAP)

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] ubiquilin 1, 10 mM TRIS, 300 mM sodium chloride (NaCl), 0.01 % sodium azide (NaN3), 1 x inhibitor cocktail (roche), 1 mM benzamidine, 10 uM ZnSO4, 10 mM DTT, 10 % D20, ...Contents: 0.5 mM [U-13C; U-15N] ubiquilin 1, 10 mM TRIS, 300 mM sodium chloride (NaCl), 0.01 % sodium azide (NaN3), 1 x inhibitor cocktail (roche), 1 mM benzamidine, 10 uM ZnSO4, 10 mM DTT, 10 % D20, 90 % H20, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMubiquilin 1-1[U-13C; U-15N]1
10 mMTRIS-21
300 mMsodium chloride (NaCl)-31
0.01 %sodium azide (NaN3)-41
1 v/vinhibitor cocktail (roche)-51
1 mMbenzamidine-61
10 uMZnSO4-71
10 mMDTT-81
10 %D20-91
90 %H20-101
Sample conditionsIonic strength: 300 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.106Goddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
FMCLemak, Steren, Llinas & Arrowsmithchemical shift assignment
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection
PSVS1.3Bhattacharya and Montelionevalidation
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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