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- PDB-1whm: Solution structure of the 2nd CAP-Gly domain in human cylindromat... -

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Basic information

Entry
Database: PDB / ID: 1whm
TitleSolution structure of the 2nd CAP-Gly domain in human cylindromatosis tumor suppressor CYLD
ComponentsCylindromatosis tumor suppressor CYLD
KeywordsANTITUMOR PROTEIN / Tumor suppressor / deubiquitinating enzyme / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / : / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip ...negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / : / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip / regulation of necroptotic process / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of JNK cascade / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / proline-rich region binding / negative regulation of non-canonical NF-kappaB signal transduction / K48-linked deubiquitinase activity / TNFR1-induced proapoptotic signaling / positive regulation of T cell differentiation / negative regulation of type I interferon production / K63-linked deubiquitinase activity / positive regulation of protein localization / positive regulation of T cell receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / necroptotic process / homeostasis of number of cells / regulation of microtubule cytoskeleton organization / regulation of mitotic cell cycle / ciliary basal body / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / spindle / negative regulation of inflammatory response / Wnt signaling pathway / regulation of inflammatory response / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / microtubule / Ub-specific processing proteases / cell cycle / innate immune response / centrosome / protein kinase binding / perinuclear region of cytoplasm / proteolysis / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Phosphorylation region of CYLD, unstructured / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site ...Phosphorylation region of CYLD, unstructured / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase CYLD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaitok, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the 2nd CAP-Gly domain in human cylindromatosis tumor suppressor CYLD
Authors: Saitok, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cylindromatosis tumor suppressor CYLD


Theoretical massNumber of molelcules
Total (without water)9,5661
Polymers9,5661
Non-polymers00
Water0
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 Cylindromatosis tumor suppressor CYLD / KIAA0849 protein


Mass: 9565.613 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free Protein synthesis / Gene: Kazusa cDNA fh04363 / Plasmid: P031006-38 / References: UniProt: Q9NQC7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM protein, 20mM sodium phosphate buffer, pH 6.0, 100mM NaCl, 2mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5Johnson, B.A.data analysis
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: simulated annealing / 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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