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- PDB-2yrb: Solution structure of the first C2 domain from human KIAA1005 protein -

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Basic information

Entry
Database: PDB / ID: 2yrb
TitleSolution structure of the first C2 domain from human KIAA1005 protein
ComponentsProtein fantom
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta sandwich / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


thromboxane A2 receptor binding / nose development / neural tube patterning / pericardium development / lateral ventricle development / establishment of planar polarity / photoreceptor connecting cilium / ciliary transition zone / corpus callosum development / olfactory bulb development ...thromboxane A2 receptor binding / nose development / neural tube patterning / pericardium development / lateral ventricle development / establishment of planar polarity / photoreceptor connecting cilium / ciliary transition zone / corpus callosum development / olfactory bulb development / non-motile cilium assembly / camera-type eye development / regulation of smoothened signaling pathway / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / determination of left/right symmetry / negative regulation of G protein-coupled receptor signaling pathway / establishment or maintenance of cell polarity / cochlea development / axoneme / bicellular tight junction / Hedgehog 'off' state / Anchoring of the basal body to the plasma membrane / cerebellum development / kidney development / liver development / cell-cell junction / in utero embryonic development / nuclear speck / ciliary basal body / cilium / centrosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RPGR-interacting protein 1, first C2 domain / RPGRIP1 family / RPGRIP1, C-terminal / First C2 domain of RPGR-interacting protein 1 / Retinitis pigmentosa G-protein regulator interacting C-terminal / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. ...RPGR-interacting protein 1, first C2 domain / RPGRIP1 family / RPGRIP1, C-terminal / First C2 domain of RPGR-interacting protein 1 / Retinitis pigmentosa G-protein regulator interacting C-terminal / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first C2 domain from human KIAA1005 protein
Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE This residue is BAA76849 in GenBank. See Ref. 3 in Q68CZ1 (FTM_HUMAN).

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein fantom


Theoretical massNumber of molelcules
Total (without water)17,6181
Polymers17,6181
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 least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein fantom / KIAA1005 protein / RPGR-interacting protein 1-like protein / RPGRIP1-like protein


Mass: 17617.586 Da / Num. of mol.: 1 / Fragment: C2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P050719-05 / References: UniProt: Q68CZ1

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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: 1.31mM uniformly 13C, 15N-labeled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3, 10% D2O, 90% H2O
Solvent system: 10% D2O / 90% H2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9822Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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