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- PDB-6fjd: Human KIBRA C2 domain mutant C771A in complex with phosphatidylin... -

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Basic information

Entry
Database: PDB / ID: 6fjd
TitleHuman KIBRA C2 domain mutant C771A in complex with phosphatidylinositol 4,5-bisphosphate
ComponentsProtein KIBRA
KeywordsLIPID BINDING PROTEIN / C2 domain / Kibra / phosphoinositide-binding / membrane interaction
Function / homology
Function and homology information


regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / kinase binding / ruffle membrane / cell migration ...regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / kinase binding / ruffle membrane / cell migration / positive regulation of MAPK cascade / transcription coactivator activity / molecular adaptor activity / negative regulation of cell population proliferation / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
WWC, C2 domain / C2 domain / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...WWC, C2 domain / C2 domain / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PBU / Protein KIBRA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.898 Å
AuthorsCrennell, S.J. / Posner, M.G. / Bagby, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BBSRC (Biotechnology and Biological Sciences Research Council)BB/J008176/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain.
Authors: Posner, M.G. / Upadhyay, A. / Ishima, R. / Kalli, A.C. / Harris, G. / Kremerskothen, J. / Sansom, M.S.P. / Crennell, S.J. / Bagby, S.
History
DepositionJan 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 27, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation
Item: _atom_site.occupancy / _citation.journal_volume ..._atom_site.occupancy / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein KIBRA
B: Protein KIBRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,48715
Polymers31,7322
Non-polymers1,75513
Water95553
1
A: Protein KIBRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,24510
Polymers15,8661
Non-polymers1,3799
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein KIBRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2425
Polymers15,8661
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.404, 83.404, 208.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-911-

HOH

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Components

#1: Protein Protein KIBRA / HBeAg-binding protein 3 / Kidney and brain protein / KIBRA / WW domain-containing protein 1


Mass: 15866.046 Da / Num. of mol.: 2 / Mutation: C771A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWC1, KIAA0869 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IX03
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PBU / (2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE / di-butanoyl L-alpha-phosphatidyl-D-myo-inositol 4,5-bisphosphate / di-C4-PIP2


Mass: 634.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H33O19P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH 8.0, 1.5M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.898→50 Å / Num. obs: 10159 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.5
Reflection shellResolution: 2.898→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.099 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.12rc0_2797: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z0U

2z0u


Resolution: 2.898→29.47 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2417 506 5.01 %
Rwork0.2028 --
obs0.2049 10100 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.898→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 107 53 2173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012152
X-RAY DIFFRACTIONf_angle_d1.0122912
X-RAY DIFFRACTIONf_dihedral_angle_d18.3281298
X-RAY DIFFRACTIONf_chiral_restr0.052339
X-RAY DIFFRACTIONf_plane_restr0.004357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8985-3.18980.291140.26092318X-RAY DIFFRACTION99
3.1898-3.65070.24651130.19952355X-RAY DIFFRACTION100
3.6507-4.59670.22771280.16962390X-RAY DIFFRACTION99
4.5967-29.47120.23341510.21262531X-RAY DIFFRACTION100

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