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- PDB-7bqf: Dimerization of SAV1 WW tandem -

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Basic information

Entry
Database: PDB / ID: 7bqf
TitleDimerization of SAV1 WW tandem
ComponentsProtein salvador homolog 1
KeywordsSIGNALING PROTEIN / Hippo pathway / WW domain / SAV1
Function / homology
Function and homology information


keratinocyte apoptotic process / Signaling by Hippo / intestinal epithelial cell differentiation / regulation of stem cell population maintenance / positive regulation of keratinocyte apoptotic process / negative regulation of cardiac muscle cell proliferation / lung epithelial cell differentiation / hippo signaling / regulation of organ growth / cardiac muscle cell proliferation ...keratinocyte apoptotic process / Signaling by Hippo / intestinal epithelial cell differentiation / regulation of stem cell population maintenance / positive regulation of keratinocyte apoptotic process / negative regulation of cardiac muscle cell proliferation / lung epithelial cell differentiation / hippo signaling / regulation of organ growth / cardiac muscle cell proliferation / ventricular septum morphogenesis / hair follicle development / positive regulation of fat cell differentiation / keratinocyte differentiation / epithelial cell proliferation / positive regulation of DNA-binding transcription factor activity / negative regulation of epithelial cell proliferation / molecular adaptor activity / protein stabilization / positive regulation of apoptotic process / negative regulation of cell population proliferation / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Scaffold protein salvador / SARAH domain / SARAH domain profile. / WW domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Protein salvador homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70037617383 Å
AuthorsLin, Z. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Cell Rep / Year: 2020
Title: A WW Tandem-Mediated Dimerization Mode of SAV1 Essential for Hippo Signaling.
Authors: Lin, Z. / Xie, R. / Guan, K. / Zhang, M.
History
DepositionMar 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 salvador homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8362
Polymers10,7481
Non-polymers881
Water1,18966
1
A: Protein salvador homolog 1
hetero molecules

A: Protein salvador homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6724
Polymers21,4962
Non-polymers1762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3610 Å2
ΔGint-7 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.715, 46.715, 83.151
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Protein salvador homolog 1 / 45 kDa WW domain protein / mWW45


Mass: 10747.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sav1, Ww45, Wwp3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VEB2
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% v/v 1,4-Dioxane, 20% w/v PEG 3350 and 100 mM Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 11842 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 27.9061568136 Å2 / CC1/2: 0.95 / Net I/σ(I): 48.6
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 602 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YSB, 2DWV

2ysb

2dwv


Resolution: 1.70037617383→27.717 Å / SU ML: 0.20145332907 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.2569718824
RfactorNum. reflection% reflection
Rfree0.219879832605 1194 10.0827562912 %
Rwork0.195975016281 --
obs0.198462671177 11842 98.1760902006 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.7549876993 Å2
Refinement stepCycle: LAST / Resolution: 1.70037617383→27.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 0 6 66 766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00678832420286733
X-RAY DIFFRACTIONf_angle_d0.9711845803881007
X-RAY DIFFRACTIONf_chiral_restr0.043095726311396
X-RAY DIFFRACTIONf_plane_restr0.00635232196708132
X-RAY DIFFRACTIONf_dihedral_angle_d12.7129014355266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7004-1.76840.2921507793561230.2392375365281104X-RAY DIFFRACTION93.5926773455
1.7684-1.84890.2565163353821260.2215030039821136X-RAY DIFFRACTION95.751138088
1.8489-1.94640.2847543751931300.2166896990021153X-RAY DIFFRACTION97.1233913702
1.9464-2.06830.2327877277331300.2095295791361162X-RAY DIFFRACTION98.4756097561
2.0683-2.22790.277071749271310.202432583541182X-RAY DIFFRACTION99.4696969697
2.2279-2.4520.2572295471331320.2089411064951194X-RAY DIFFRACTION99.4748687172
2.452-2.80650.2321225817961360.2150901519471203X-RAY DIFFRACTION99.9253731343
2.8065-3.53470.2103166617581420.2095141887621226X-RAY DIFFRACTION100
3.5347-27.70.1864627490861440.1691176916711288X-RAY DIFFRACTION99.652052888
Refinement TLS params.Method: refined / Origin x: -3.76667466183 Å / Origin y: -8.05053562377 Å / Origin z: 22.7085063647 Å
111213212223313233
T0.194777051606 Å2-0.0104941726198 Å20.0129581478542 Å2-0.186988306889 Å20.0454841959731 Å2--0.180139383345 Å2
L1.04895608906 °20.510029215002 °20.0679922630015 °2-4.60134985755 °21.09623841422 °2--2.21128349477 °2
S0.0388635268529 Å °0.00342381169159 Å °-0.0566652312404 Å °0.144115038928 Å °0.135348547784 Å °-0.0196496654009 Å °0.0865220870935 Å °-0.232268321447 Å °-0.108139127858 Å °
Refinement TLS groupSelection details: all

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