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- PDB-6bn1: Salvador Hippo SARAH domain complex -

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Basic information

Entry
Database: PDB / ID: 6bn1
TitleSalvador Hippo SARAH domain complex
Components
  • Scaffold protein salvador
  • Serine/threonine-protein kinase hippo
KeywordsSIGNALING PROTEIN / Hippo
Function / homology
Function and homology information


Formation of the Hippo kinase cassette / Phosphorylation-dependent inhibition of YKI / Phosphorylation-independent inhibition of YKI / apicomedial cortex / Malpighian tubule development / R8 cell fate specification / imaginal disc development / DS ligand bound to FT receptor / regulation of imaginal disc growth / compound eye morphogenesis ...Formation of the Hippo kinase cassette / Phosphorylation-dependent inhibition of YKI / Phosphorylation-independent inhibition of YKI / apicomedial cortex / Malpighian tubule development / R8 cell fate specification / imaginal disc development / DS ligand bound to FT receptor / regulation of imaginal disc growth / compound eye morphogenesis / morphogenesis of an epithelial sheet / border follicle cell migration / protein serine/threonine kinase activity => GO:0004674 / retinal cell programmed cell death / negative regulation of organ growth / eye development / hippo signaling / regulation of apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / regulation of protein processing / stress-activated protein kinase signaling cascade / negative regulation of glial cell proliferation / negative regulation of multicellular organism growth / negative regulation of neuroblast proliferation / organ growth / regulation of dendrite morphogenesis / response to ionizing radiation / activation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / stem cell proliferation / stem cell differentiation / peptidyl-threonine phosphorylation / negative regulation of canonical Wnt signaling pathway / apical part of cell / regulation of cell population proliferation / negative regulation of neuron apoptotic process / protein autophosphorylation / molecular adaptor activity / non-specific serine/threonine protein kinase / positive regulation of apoptotic process / apical plasma membrane / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / signal transduction / protein homodimerization activity / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Scaffold protein salvador / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / WW domain / WW domain superfamily / WW/rsp5/WWP domain profile. ...Scaffold protein salvador / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / WW domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Few Secondary Structures / Irregular / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Serine/threonine-protein kinase hippo / Scaffold protein salvador
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsCairns, L. / Kavran, J.M.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Salvador has an extended SARAH domain that mediates binding to Hippo kinase.
Authors: Cairns, L. / Tran, T. / Fowl, B.H. / Patterson, A. / Kim, Y.J. / Bothner, B. / Kavran, J.M.
History
DepositionNov 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase hippo
B: Scaffold protein salvador
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8027
Polymers15,2712
Non-polymers5315
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-66 kcal/mol
Surface area8640 Å2
2
A: Serine/threonine-protein kinase hippo
hetero molecules

A: Serine/threonine-protein kinase hippo
hetero molecules

B: Scaffold protein salvador
hetero molecules

B: Scaffold protein salvador
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,60414
Polymers30,5414
Non-polymers1,06310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation3_564-y,x+1,z-1/41
crystal symmetry operation7_565y,x+1,-z+1/41
Buried area5660 Å2
ΔGint-108 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.934, 49.934, 186.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Serine/threonine-protein kinase hippo / Drosophila homolog of MST1 and MST2 / STE20-like kinase MST / dMST


Mass: 6936.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: hpo, CG11228 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8T0S6, non-specific serine/threonine protein kinase
#2: Protein Scaffold protein salvador / Shar-pei


Mass: 8333.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sav, SHRP, CG33193 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VCR6
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM Sodium Cacadylate 35% MPD 2% PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→38.903 Å / Num. obs: 7868 / % possible obs: 100 % / Redundancy: 24.4 % / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.6→38.903 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8
RfactorNum. reflection% reflection
Rfree0.2459 384 4.9 %
Rwork0.202 --
obs0.2042 7836 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 33 34 1114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071094
X-RAY DIFFRACTIONf_angle_d0.9521464
X-RAY DIFFRACTIONf_dihedral_angle_d17.536425
X-RAY DIFFRACTIONf_chiral_restr0.038154
X-RAY DIFFRACTIONf_plane_restr0.005185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.97640.33661280.28442388X-RAY DIFFRACTION99
2.9764-3.74940.27351220.22022442X-RAY DIFFRACTION99
3.7494-38.90750.221340.17852622X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.3063 Å / Origin y: 16.6109 Å / Origin z: 19.8501 Å
111213212223313233
T0.5494 Å20.0711 Å20.0084 Å2-0.5184 Å20.0364 Å2--0.4907 Å2
L1.9214 °20.4962 °2-1.2679 °2-1.0415 °2-2.0079 °2--7.6123 °2
S0.0057 Å °-0.0577 Å °0.0711 Å °0.1227 Å °-0.0775 Å °-0.0095 Å °0.131 Å °0.4889 Å °0.0149 Å °
Refinement TLS groupSelection details: chain A or chain B

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