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- PDB-6j69: Structure of KIBRA and Dendrin Complex -

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Basic information

Entry
Database: PDB / ID: 6j69
TitleStructure of KIBRA and Dendrin Complex
Components
  • Peptide from Dendrin
  • Protein KIBRA
KeywordsCELL CYCLE / Tandem WW domain / Tandem PY motif / HIPPO Signaling
Function / homology
Function and homology information


regulation of hippo signaling / Signaling by Hippo / negative regulation of organ growth / dendritic spine membrane / negative regulation of hippo signaling / kinase binding / ruffle membrane / cell migration / protein-macromolecule adaptor activity / perikaryon ...regulation of hippo signaling / Signaling by Hippo / negative regulation of organ growth / dendritic spine membrane / negative regulation of hippo signaling / kinase binding / ruffle membrane / cell migration / protein-macromolecule adaptor activity / perikaryon / postsynaptic membrane / positive regulation of MAPK cascade / molecular adaptor activity / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / dendrite / endoplasmic reticulum membrane / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dendrin / Nephrin and CD2AP-binding protein, Dendrin / WWC, C2 domain / : / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily ...Dendrin / Nephrin and CD2AP-binding protein, Dendrin / WWC, 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
Similarity search - Domain/homology
Protein KIBRA / Dendrin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.753 Å
AuthorsLin, Z. / Yang, Z. / Ji, Z. / Zhang, M.
CitationJournal: Cell Rep / Year: 2019
Title: Kibra Modulates Learning and Memory via Binding to Dendrin.
Authors: Ji, Z. / Li, H. / Yang, Z. / Huang, X. / Ke, X. / Ma, S. / Lin, Z. / Lu, Y. / Zhang, M.
History
DepositionJan 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Peptide from Dendrin


Theoretical massNumber of molelcules
Total (without water)18,7882
Polymers18,7882
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.443, 85.443, 80.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-50-

CYS

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Components

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


Mass: 16036.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wwc1, Kiaa0869 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q5SXA9
#2: Protein/peptide Peptide from Dendrin


Mass: 2751.083 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ddn, Gm748, Kiaa0749 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q80TS7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES, 0.4M Sodium citrate, 16% 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2.753→50 Å / Num. obs: 8167 / % possible obs: 99.8 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 38.6
Reflection shellResolution: 2.753→2.8 Å / Rmerge(I) obs: 0.92 / Num. unique obs: 391

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J68

6j68


Resolution: 2.753→42.721 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.95
RfactorNum. reflection% reflection
Rfree0.2824 367 4.91 %
Rwork0.2361 --
obs0.2386 7481 91.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.753→42.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 0 13 1158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111182
X-RAY DIFFRACTIONf_angle_d1.2011615
X-RAY DIFFRACTIONf_dihedral_angle_d16.836429
X-RAY DIFFRACTIONf_chiral_restr0.051166
X-RAY DIFFRACTIONf_plane_restr0.007216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7532-3.15150.3711840.31221915X-RAY DIFFRACTION75
3.1515-3.97010.33831390.25992509X-RAY DIFFRACTION99
3.9701-42.72660.22931440.20172690X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.5853 Å / Origin y: 89.9668 Å / Origin z: 18.6998 Å
111213212223313233
T0.4025 Å20.0243 Å2-0.0214 Å2-0.2732 Å20.0584 Å2--0.3634 Å2
L1.4461 °20.1858 °20.2553 °2-0.1988 °20.0199 °2--0.0353 °2
S0.0494 Å °-0.149 Å °-0.1259 Å °0.3295 Å °-0.0955 Å °-0.0713 Å °-0.0538 Å °-0.0551 Å °0.0255 Å °
Refinement TLS groupSelection details: all

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