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- PDB-6fb4: human KIBRA C2 domain mutant C771A -

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Basic information

Entry
Database: PDB / ID: 6fb4
Titlehuman KIBRA C2 domain mutant C771A
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 / ruffle membrane / kinase binding / 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 / ruffle membrane / kinase binding / 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
PHOSPHATE ION / Protein KIBRA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4156309909 Å
AuthorsCrennell, S.J. / Posner, M.G. / Bagby, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/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
DepositionDec 18, 2017Deposition 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5597
Polymers29,0952
Non-polymers4635
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-7 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.880, 83.880, 207.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-947-

HOH

21A-952-

HOH

31A-959-

HOH

41A-960-

HOH

51B-943-

HOH

61B-962-

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: 14547.594 Da / Num. of mol.: 2 / Mutation: C771A
Source method: isolated from a genetically manipulated source
Details: KIBRA is a multi-functional scaffold protein, the C2 domain binds phosphoinositides.
Source: (gene. exp.) Homo sapiens (human) / Gene: WWC1, KIAA0869 / Organ: kidney, brain / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IX03
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.63 Å3/Da / Density % sol: 66.08 % / Description: pavilion
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Na HEPES, 0.8M Na dihydrogen phosphare, 0.8M K dihydrogen phosphate 5% glycerol cryoprotectant

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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: Sep 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.415→72.643 Å / Num. obs: 17355 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 41.2630665184 Å2 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.14 / Χ2: 0.96 / Net I/σ(I): 10.7
Reflection shellResolution: 2.42→2.5 Å / Redundancy: 6.22 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.7 / Rrim(I) all: 0.676 / Χ2: 1.34 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
d*TREKdata reduction
d*TREKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9D

3k9d


Resolution: 2.4156309909→72.6422108694 Å / SU ML: 0.325016801318 / Cross valid method: FREE R-VALUE / σ(F): 1.35109357799 / Phase error: 25.3297439476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.247460327115 859 4.95500692201 %random selection
Rwork0.200800854876 16477 --
obs0.203125005734 17336 99.7124122857 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.639236193 Å2
Refinement stepCycle: LAST / Resolution: 2.4156309909→72.6422108694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 29 124 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01028838710412120
X-RAY DIFFRACTIONf_angle_d1.000204577612872
X-RAY DIFFRACTIONf_chiral_restr0.0515261468511336
X-RAY DIFFRACTIONf_plane_restr0.00453971766486364
X-RAY DIFFRACTIONf_dihedral_angle_d13.07632847941304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4156-2.5670.3619660763051240.2720168469362647X-RAY DIFFRACTION99.0350250179
2.567-2.76520.3004887571011540.2760535735422671X-RAY DIFFRACTION99.7528248588
2.7652-3.04350.301289747961350.2619662936892704X-RAY DIFFRACTION100
3.0435-3.48390.2755957488951560.2059561527332716X-RAY DIFFRACTION100
3.4839-4.38920.2332043311591340.1605786330892785X-RAY DIFFRACTION99.9657534247
4.3892-72.6750.188259525061560.1777595461732954X-RAY DIFFRACTION99.52

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