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- PDB-1ixd: Solution structure of the CAP-GLY domain from human cylindromatos... -

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Basic information

Entry
Database: PDB / ID: 1ixd
TitleSolution structure of the CAP-GLY domain from human cylindromatosis tomour-suppressor CYLD
ComponentsCylindromatosis tumour-suppressor CYLD
KeywordsANTITUMOR PROTEIN / Structural genomics / Tumour suppressor / 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 / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of extrinsic apoptotic signaling pathway / proline-rich region binding / 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 / negative regulation of NF-kappaB transcription factor activity / positive regulation of T cell receptor signaling pathway / 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 / NOD1/2 Signaling Pathway / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / negative regulation of inflammatory response / spindle / regulation of inflammatory response / microtubule / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / 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
AuthorsSaito, K. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: STRUCTURE / Year: 2004
Title: The CAP-Gly domain of CYLD associates with the proline-rich sequence in NEMO/IKKgamma
Authors: Saito, K. / Kigawa, T. / Koshiba, S. / Sato, K. / Matsuo, Y. / Sakamoto, A. / Takagi, T. / Shirouzu, M. / Yabuki, T. / Nunokawa, E. / Seki, E. / Matsuda, T. / Aoki, M. / Miyata, Y. / ...Authors: Saito, K. / Kigawa, T. / Koshiba, S. / Sato, K. / Matsuo, Y. / Sakamoto, A. / Takagi, T. / Shirouzu, M. / Yabuki, T. / Nunokawa, E. / Seki, E. / Matsuda, T. / Aoki, M. / Miyata, Y. / Hirakawa, N. / Inoue, M. / Terada, T. / Nagase, T. / Kikuno, R. / Nakayama, M. / Ohara, O. / Tanaka, A. / Yokoyama, S.
History
DepositionJun 19, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET determination method: author determined THE STRAND OF TYR33-GLY40 CONTAINS BULGE STRUCTURE AT ARG37

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cylindromatosis tumour-suppressor CYLD


Theoretical massNumber of molelcules
Total (without water)10,8711
Polymers10,8711
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cylindromatosis tumour-suppressor CYLD / Probable ubiquitin carboxyl-terminal hydrolase CYLD / Ubiquitin thiolesterase CYLD / Ubiquitin- ...Probable ubiquitin carboxyl-terminal hydrolase CYLD / Ubiquitin thiolesterase CYLD / Ubiquitin-specific processing protease CYLD / Deubiquitinating enzyme CYLD / HSPC057


Mass: 10871.257 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: fh04363 / Plasmid: P011213-03 / References: UniProt: Q9NQC7, EC: 3.1.2.15

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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: 0.8mM CAP-GLY domain U-15N,13C; 20mM phosphate buffer Na; 100MM SODIUM CHLORIDE; 1MM DITHIOTHREITOL; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 6.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Deraglio, F.processing
NMRView5Johnson, B.data analysis
CNS1.1Brunger, A.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: 200 / Conformers submitted total number: 20

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