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- PDB-7bqg: Complex structure of SAV1 and Dendrin -

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Basic information

Entry
Database: PDB / ID: 7bqg
TitleComplex structure of SAV1 and Dendrin
ComponentsProtein salvador homolog 1,Dendrin
KeywordsSIGNALING PROTEIN / Hippo pathway / WW domain / SAV1 / Dendrin
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 / dendritic spine membrane ...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 / dendritic spine membrane / cardiac muscle cell proliferation / ventricular septum morphogenesis / hair follicle development / positive regulation of fat cell differentiation / keratinocyte differentiation / epithelial cell proliferation / cell projection / positive regulation of DNA-binding transcription factor activity / negative regulation of epithelial cell proliferation / perikaryon / postsynaptic membrane / molecular adaptor activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / dendrite / endoplasmic reticulum membrane / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dendrin / Scaffold protein salvador / Nephrin and CD2AP-binding protein, Dendrin / 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
: / Dendrin / Protein salvador homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55010861961 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,Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4384
Polymers10,3201
Non-polymers1173
Water1,65792
1
A: Protein salvador homolog 1,Dendrin
hetero molecules

A: Protein salvador homolog 1,Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8758
Polymers20,6412
Non-polymers2356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.803, 43.084, 99.385
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

K

21A-303-

K

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Components

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


Mass: 10320.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sav1, Ww45, Wwp3, Ddn, Gm748, Kiaa0749 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VEB2, UniProt: Q80TS7
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% w/v PEG 2000 MME and 100 mM BIS-TRIS propane (pH 9.0)

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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: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 11875 / % possible obs: 99.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 12.8744218645 Å2 / CC1/2: 0.99 / Net I/σ(I): 39.1
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 599 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BQF

7bqf


Resolution: 1.55010861961→49.6925 Å / SU ML: 0.149561517705 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.1462025962
RfactorNum. reflection% reflection
Rfree0.216578983246 1189 10.0126315789 %
Rwork0.177694973739 --
obs0.181655015371 11875 95.220912517 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.5003240728 Å2
Refinement stepCycle: LAST / Resolution: 1.55010861961→49.6925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms696 0 3 92 791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624081380489753
X-RAY DIFFRACTIONf_angle_d1.03131247291043
X-RAY DIFFRACTIONf_chiral_restr0.037720092214297
X-RAY DIFFRACTIONf_plane_restr0.00521105024004139
X-RAY DIFFRACTIONf_dihedral_angle_d12.1452183019271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5502-1.62070.2697638954351240.2261281519721096X-RAY DIFFRACTION79.2722547109
1.6207-1.70610.271494715081390.192501708671272X-RAY DIFFRACTION92.3429319372
1.7061-1.8130.2463161694041480.1761827590481318X-RAY DIFFRACTION95.5671447197
1.813-1.9530.2244942620831510.1739210871671349X-RAY DIFFRACTION97.0245795602
1.953-2.14950.2008243821431530.1611185123741370X-RAY DIFFRACTION99.3476842792
2.1495-2.46060.2079246788061540.1883167573051387X-RAY DIFFRACTION98.7820512821
2.4606-3.10.2477124739731560.2003697294591412X-RAY DIFFRACTION99.872611465
3.1-490.1871014137221640.1595662675121482X-RAY DIFFRACTION99.0969295605
Refinement TLS params.Method: refined / Origin x: 38.4734067236 Å / Origin y: 12.2274488768 Å / Origin z: 17.0675130407 Å
111213212223313233
T0.0918675070246 Å20.0108181817598 Å2-0.0053059500598 Å2-0.106702545478 Å20.00328914767923 Å2--0.120246215607 Å2
L0.0921946759338 °2-0.0694245414299 °2-0.337143663745 °2-0.206491020959 °20.157191144039 °2--1.22545382743 °2
S0.0316861378955 Å °-0.0101535419496 Å °-0.0383063312652 Å °-0.00596067531414 Å °-0.0116562721868 Å °0.00915819934473 Å °-0.0468093238617 Å °-0.0844047060775 Å °-0.024930326036 Å °
Refinement TLS groupSelection details: all

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