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- PDB-6jjy: Crystal Structure of KIBRA and beta-Dystroglycan -

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Basic information

Entry
Database: PDB / ID: 6jjy
TitleCrystal Structure of KIBRA and beta-Dystroglycan
Components
  • Peptide from Dystroglycan
  • Protein KIBRA
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / PTPN14
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / retrograde trans-synaptic signaling by trans-synaptic protein complex / Signaling by Hippo / O-linked glycosylation / contractile ring ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / retrograde trans-synaptic signaling by trans-synaptic protein complex / Signaling by Hippo / O-linked glycosylation / contractile ring / calcium-dependent cell-matrix adhesion / morphogenesis of an epithelial sheet / microtubule anchoring / dystrophin-associated glycoprotein complex / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / photoreceptor ribbon synapse / negative regulation of organ growth / nerve development / basement membrane organization / dystroglycan binding / positive regulation of myelination / cellular response to cholesterol / hippo signaling / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / branching involved in salivary gland morphogenesis / skeletal muscle tissue regeneration / Formation of the dystrophin-glycoprotein complex (DGC) / costamere / commissural neuron axon guidance / myelination in peripheral nervous system / node of Ranvier / angiogenesis involved in wound healing / axon regeneration / structural constituent of muscle / positive regulation of cell-matrix adhesion / response to muscle activity / regulation of synapse organization / epithelial tube branching involved in lung morphogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / alpha-actinin binding / membrane protein ectodomain proteolysis / positive regulation of oligodendrocyte differentiation / basement membrane / Non-integrin membrane-ECM interactions / plasma membrane raft / ECM proteoglycans / negative regulation of hippo signaling / postsynaptic cytosol / heart morphogenesis / negative regulation of MAPK cascade / laminin binding / signaling adaptor activity / extracellular matrix organization / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / tubulin binding / SH2 domain binding / nuclear periphery / axon guidance / negative regulation of cell migration / morphogenesis of an epithelium / filopodium / adherens junction / cellular response to mechanical stimulus / response to peptide hormone / sarcolemma / regulation of synaptic plasticity / GABA-ergic synapse / Golgi lumen / kinase binding / ruffle membrane / Regulation of expression of SLITs and ROBOs / cell migration / lamellipodium / protein transport / : / virus receptor activity / actin binding / basolateral plasma membrane / postsynaptic membrane / transcription coactivator activity / cytoskeleton / positive regulation of MAPK cascade / endoplasmic reticulum lumen / Golgi membrane / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
WWC, C2 domain / : / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. ...WWC, C2 domain / : / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Putative Ig domain / Cadherin-like superfamily / C2 domain / WW domain / C2 domain / C2 domain profile. / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Dystroglycan 1 / Protein KIBRA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsLin, Z. / Yang, Z. / Ji, Z. / Zhang, M.
CitationJournal: Elife / Year: 2019
Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.
Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 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
U: Peptide from Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5274
Polymers18,3352
Non-polymers1922
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.483, 73.483, 105.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

31U-901-

SO4

41U-901-

SO4

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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 (E. coli) / References: UniProt: Q5SXA9
#2: Protein/peptide Peptide from Dystroglycan / Dystrophin-associated glycoprotein 1


Mass: 2298.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14118
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 4.48 Å3/Da / Density % sol: 72.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 3.0-4.0M NaCl, 100mM Bis-Tris (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15114 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 40
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 724 / % possible all: 100

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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: 2.298→40.571 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1439 10 %
Rwork0.2056 --
obs0.2103 14386 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.298→40.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 10 75 1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091249
X-RAY DIFFRACTIONf_angle_d1.1011711
X-RAY DIFFRACTIONf_dihedral_angle_d15.926467
X-RAY DIFFRACTIONf_chiral_restr0.04174
X-RAY DIFFRACTIONf_plane_restr0.006229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2976-2.37970.34891310.27721142X-RAY DIFFRACTION86
2.3797-2.4750.29931350.25281164X-RAY DIFFRACTION88
2.475-2.58760.25471360.24481215X-RAY DIFFRACTION91
2.5876-2.7240.29021330.24821268X-RAY DIFFRACTION93
2.724-2.89460.31171400.26651284X-RAY DIFFRACTION96
2.8946-3.1180.29041500.24871344X-RAY DIFFRACTION98
3.118-3.43160.32391490.22011342X-RAY DIFFRACTION99
3.4316-3.92780.21711530.18141357X-RAY DIFFRACTION99
3.9278-4.94730.19741530.1591387X-RAY DIFFRACTION99
4.9473-40.57760.21531590.16831444X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -94.2259 Å / Origin y: 65.4788 Å / Origin z: 127.1158 Å
111213212223313233
T0.3127 Å20.0122 Å20.0522 Å2-0.2697 Å20.0342 Å2--0.3133 Å2
L0.7193 °20.5142 °2-1.4105 °2--0.0379 °2-0.6824 °2--2.6504 °2
S-0.1048 Å °-0.0338 Å °0.0505 Å °0.1623 Å °0.0939 Å °0.0559 Å °0.1397 Å °-0.1175 Å °0.0396 Å °
Refinement TLS groupSelection details: ALL

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