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- PDB-2cp0: Solution structure of the 1st CAP-Gly domain in human CLIP-170-re... -

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Basic information

Entry
Database: PDB / ID: 2cp0
TitleSolution structure of the 1st CAP-Gly domain in human CLIP-170-related protein CLIPR59
ComponentsCLIPR-59 protein
KeywordsPROTEIN BINDING / microtubule binding / cytoskeleton associated protein / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / ganglioside binding / peptidyl-L-cysteine S-palmitoylation / membrane biogenesis / microtubule plus-end / Golgi stack / microtubule plus-end binding / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of glucose transmembrane transport / negative regulation of microtubule polymerization ...: / ganglioside binding / peptidyl-L-cysteine S-palmitoylation / membrane biogenesis / microtubule plus-end / Golgi stack / microtubule plus-end binding / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of glucose transmembrane transport / negative regulation of microtubule polymerization / positive regulation of endocytosis / fat cell differentiation / cytoplasmic microtubule organization / trans-Golgi network membrane / Regulation of TNFR1 signaling / positive regulation of protein localization to plasma membrane / trans-Golgi network / recycling endosome membrane / microtubule binding / early endosome membrane / positive regulation of protein phosphorylation / positive regulation of apoptotic process / membrane raft / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Domain of unknown function DUF3447 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...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 / Domain of unknown function DUF3447 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CAP-Gly domain-containing linker protein 3 / CAP-Gly domain-containing linker protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the 1st CAP-Gly domain in human CLIP-170-related protein CLIPR59
Authors: Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: CLIPR-59 protein


Theoretical massNumber of molelcules
Total (without water)9,6321
Polymers9,6321
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 #20lowest energy

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Components

#1: Protein CLIPR-59 protein / CLIPR59


Mass: 9631.751 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: IOH13590 / Plasmid: P040830-02 / References: UniProt: Q96C99, UniProt: Q96DZ5*PLUS

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1mM protein, 20mM d-Tris-HCl, pH7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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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