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- PDB-6jjw: Crystal Structure of KIBRA and PTPN14 complex -

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Basic information

Entry
Database: PDB / ID: 6jjw
TitleCrystal Structure of KIBRA and PTPN14 complex
Components
  • Peptide from Tyrosine-protein phosphatase non-receptor type 14
  • Protein KIBRA
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / PTPN14
Function / homology
Function and homology information


regulation of hippo signaling / Signaling by Hippo / lymphangiogenesis / positive regulation of hippo signaling / negative regulation of organ growth / hippo signaling / regulation of protein export from nucleus / Interleukin-37 signaling / protein dephosphorylation / negative regulation of hippo signaling ...regulation of hippo signaling / Signaling by Hippo / lymphangiogenesis / positive regulation of hippo signaling / negative regulation of organ growth / hippo signaling / regulation of protein export from nucleus / Interleukin-37 signaling / protein dephosphorylation / negative regulation of hippo signaling / postsynaptic density, intracellular component / protein-tyrosine-phosphatase / signaling adaptor activity / protein tyrosine phosphatase activity / transcription coregulator activity / receptor tyrosine kinase binding / kinase binding / ruffle membrane / cell migration / protein-macromolecule adaptor activity / molecular adaptor activity / cytoskeleton / transcription coactivator activity / positive regulation of MAPK cascade / 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 / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / WWC1-like, helical hairpin / Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / WWC, C2 domain / : / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal ...: / WWC1-like, helical hairpin / Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / WWC, C2 domain / : / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein 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 / FERM central domain / WW domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / C2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Tyrosine-protein phosphatase non-receptor type 14 / Protein KIBRA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 Tyrosine-protein phosphatase non-receptor type 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,19415
Polymers19,6562
Non-polymers53813
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-80 kcal/mol
Surface area7530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.630, 107.630, 107.832
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-207-

GOL

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AU

#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 Tyrosine-protein phosphatase non-receptor type 14 / Protein-tyrosine phosphatase pez


Mass: 3619.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN14, PEZ, PTPD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15678

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Non-polymers , 5 types, 45 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 700mM magnesium formate, 100mM Bis-Tris Propane (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 9608 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 18.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 397 / % 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: 2.4→35.944 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.87
RfactorNum. reflection% reflection
Rfree0.242 445 4.75 %
Rwork0.1868 --
obs0.1895 9363 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 24 32 960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008944
X-RAY DIFFRACTIONf_angle_d0.9841279
X-RAY DIFFRACTIONf_dihedral_angle_d14.263348
X-RAY DIFFRACTIONf_chiral_restr0.039129
X-RAY DIFFRACTIONf_plane_restr0.006169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3934-2.73960.28741390.22262747X-RAY DIFFRACTION92
2.7396-3.45110.25481540.21453039X-RAY DIFFRACTION100
3.4511-35.9480.22471520.16443132X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 71.346 Å / Origin y: 83.2853 Å / Origin z: -63.4495 Å
111213212223313233
T0.3327 Å20.0419 Å20.0592 Å2-0.2817 Å2-0.0806 Å2--0.2563 Å2
L5.1788 °2-0.1678 °2-0.9919 °2-1.1967 °2-0.2378 °2--1.2016 °2
S0.01 Å °-0.1823 Å °0.0014 Å °-0.1279 Å °0.0731 Å °-0.1483 Å °0.0567 Å °0.1841 Å °-0.0675 Å °
Refinement TLS groupSelection details: all

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