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- PDB-1x5m: Solution structure of the core domain of calcyclin binding protei... -

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Basic information

Entry
Database: PDB / ID: 1x5m
TitleSolution structure of the core domain of calcyclin binding protein; siah-interacting protein (SIP)
ComponentsCalcyclin-binding protein
KeywordsAPOPTOSIS / SIGNALING PROTEIN / CS domain / Calcyclin-binding protein/Siah-interacting protein/S100A6-binding protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


beta-catenin destruction complex / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / tubulin binding / cellular response to leukemia inhibitory factor / heart development / protein domain specific binding / ubiquitin protein ligase binding / protein homodimerization activity ...beta-catenin destruction complex / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / tubulin binding / cellular response to leukemia inhibitory factor / heart development / protein domain specific binding / ubiquitin protein ligase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / : / Siah interacting protein, N terminal / SGS domain / SGS domain / SGS domain profile. / CS domain / CS domain ...Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / : / Siah interacting protein, N terminal / SGS domain / SGS domain / SGS domain profile. / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Calcyclin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.R. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the core domain of calcyclin binding protein; siah-interacting protein (SIP)
Authors: Qin, X.R. / Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2005Provider: 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_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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcyclin-binding protein


Theoretical massNumber of molelcules
Total (without water)14,0781
Polymers14,0781
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
Representative

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Components

#1: Protein Calcyclin-binding protein / CacyBP / hCacyBP / Siah-interacting protein / S100A6-binding protein / PNAS-107


Mass: 14078.024 Da / Num. of mol.: 1 / Fragment: CS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: CACYBP, S100A6BP, SIP / Plasmid: p040329-62 / References: UniProt: Q9HB71

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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: 0.98mM 13C,15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9296Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.structure solution
CYANA1.0.7Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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