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- PDB-6xa6: Crystal Structure of Human Scribble PDZ3:Vangl2 Complex -

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Basic information

Entry
Database: PDB / ID: 6xa6
TitleCrystal Structure of Human Scribble PDZ3:Vangl2 Complex
Components
  • Protein scribble homolog
  • Vang-like protein 2
KeywordsCYTOSOLIC PROTEIN / Cell polarity
Function / homology
Function and homology information


cell migration involved in kidney development / establishment of planar polarity involved in neural tube closure / orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis / planar dichotomous subdivision of terminal units involved in lung branching morphogenesis / lateral sprouting involved in lung morphogenesis / dopaminergic neuron axon guidance / serotonergic neuron axon guidance / regulation of establishment of planar polarity / apical cytoplasm / establishment of body hair planar orientation ...cell migration involved in kidney development / establishment of planar polarity involved in neural tube closure / orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis / planar dichotomous subdivision of terminal units involved in lung branching morphogenesis / lateral sprouting involved in lung morphogenesis / dopaminergic neuron axon guidance / serotonergic neuron axon guidance / regulation of establishment of planar polarity / apical cytoplasm / establishment of body hair planar orientation / muscular septum morphogenesis / convergent extension involved in axis elongation / kidney morphogenesis / convergent extension involved in neural plate elongation / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / establishment of planar polarity / cochlear nucleus development / cell pole / apoptotic process involved in morphogenesis / heparan sulfate proteoglycan biosynthetic process / astrocyte cell migration / Scrib-APC-beta-catenin complex / myelin sheath abaxonal region / inner ear receptor cell stereocilium organization / synaptic vesicle targeting / establishment of apical/basal cell polarity / polarized epithelial cell differentiation / somatic stem cell division / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / membranous septum morphogenesis / regulation of synapse pruning / cochlea morphogenesis / mammary gland duct morphogenesis / cell-cell contact zone / protein localization to adherens junction / establishment or maintenance of epithelial cell apical/basal polarity / post-anal tail morphogenesis / activation of GTPase activity / glomerulus development / COPII-coated ER to Golgi transport vesicle / non-motile cilium assembly / PCP/CE pathway / auditory receptor cell stereocilium organization / apical protein localization / regulation of Wnt signaling pathway / negative regulation of mitotic cell cycle / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / RND2 GTPase cycle / RND3 GTPase cycle / digestive tract morphogenesis / positive chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / heart looping / receptor clustering / RHOJ GTPase cycle / negative regulation of activated T cell proliferation / RHOQ GTPase cycle / positive regulation of receptor recycling / CDC42 GTPase cycle / lateral plasma membrane / immunological synapse / somatic stem cell population maintenance / synaptic vesicle endocytosis / hair follicle development / Rho protein signal transduction / stress fiber / signaling adaptor activity / Asymmetric localization of PCP proteins / adherens junction / regulation of actin cytoskeleton organization / neural tube closure / wound healing / cell-cell adhesion / postsynaptic density membrane / positive regulation of type II interferon production / cell-cell junction / cell junction / cell migration / presynapse / lamellipodium / basolateral plasma membrane / cell population proliferation / postsynaptic density / positive regulation of apoptotic process / apical plasma membrane / cadherin binding / protein kinase binding / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Vang-like protein / Strabismus protein / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Vang-like protein / Strabismus protein / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein scribble homolog / Vang-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHow, J.Y. / Kvansakul, M.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1079133 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Biochem.J. / Year: 2021
Title: Structural basis of the human Scribble-Vangl2 association in health and disease.
Authors: How, J.Y. / Stephens, R.K. / Lim, K.Y.B. / Humbert, P.O. / Kvansakul, M.
History
DepositionJun 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
B: Protein scribble homolog
C: Vang-like protein 2
A: Protein scribble homolog
D: Vang-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0675
Polymers22,0054
Non-polymers621
Water1,22568
1
B: Protein scribble homolog
C: Vang-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0653
Polymers11,0032
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-2 kcal/mol
Surface area5190 Å2
MethodPISA
2
A: Protein scribble homolog
D: Vang-like protein 2


Theoretical massNumber of molelcules
Total (without water)11,0032
Polymers11,0032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-2 kcal/mol
Surface area5300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.706, 54.706, 129.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein Protein scribble homolog / hScrib / Protein LAP4


Mass: 10082.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli (E. coli) / References: UniProt: Q14160
#2: Protein/peptide Vang-like protein 2 / Loop-tail protein 1 homolog / Strabismus 1 / Van Gogh-like protein 2


Mass: 920.000 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULK5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.8 and 66% (v/v) MPD

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9357 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9357 Å / Relative weight: 1
ReflectionResolution: 1.95→37.08 Å / Num. obs: 15107 / % possible obs: 99.88 % / Redundancy: 27.6 % / Biso Wilson estimate: 34.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 38.36
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 5.54 / Num. unique obs: 1475 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WYU

4wyu


Resolution: 1.95→37.08 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2533 778 5.15 %
Rwork0.2166 14323 -
obs0.2185 15101 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.61 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 4 68 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931335
X-RAY DIFFRACTIONf_angle_d1.15471794
X-RAY DIFFRACTIONf_chiral_restr0.0545216
X-RAY DIFFRACTIONf_plane_restr0.0062238
X-RAY DIFFRACTIONf_dihedral_angle_d20.3659503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.070.28821180.22562341X-RAY DIFFRACTION99.96
2.07-2.230.25321300.21112322X-RAY DIFFRACTION99.96
2.23-2.460.29881230.21622343X-RAY DIFFRACTION99.96
2.46-2.810.28521460.22892346X-RAY DIFFRACTION99.92
2.81-3.540.26361270.2252417X-RAY DIFFRACTION100
3.54-37.080.22431340.20892554X-RAY DIFFRACTION99.63
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.366196512260.3010076888890.646839293394.687846074390.4101927087724.73748908890.4359587232710.1856377645890.14648719919-1.076148872120.04012806640450.403222479503-0.6460532722111.119323631-0.1976616882240.377614916747-0.0600283783377-0.03057480592410.7941035618140.1414581079480.546428343209-4.412491112228.11731490767-10.4992930013
26.3234464818-1.150888894411.541938085825.182696688280.8349318675465.91824488885-0.2016536926460.000328111928115-0.0190374878114-0.06543505170990.236096954623-0.090778158671-0.150162184396-0.215241042612-0.1931898574060.191548985625-0.0260054005334-0.01852965603230.3951775581580.08038511494990.278614771295-14.50052642662.91285847636-8.85240841353
36.70717159813-0.04534067950491.181242391298.30213350075-2.459106642334.51935838754-0.2772676759160.6685594484211.093935653570.1689737077310.230290812837-1.48771064251-0.1753101851860.3304621976660.1780318838380.1314448957860.0202798973725-0.07607187043080.3851270113970.04408351866570.309424827856-7.625186677046.72258453451-8.15442151239
44.806355965412.36554384105-1.242995912882.10837063754-1.867803886995.81460358977-0.05808265153920.477857009574-0.453185151278-0.5430907983230.4476961405290.7334402592470.283391356436-0.1205209241-0.3785754605560.206150771612-0.0391521076134-0.04536637634780.4650869850770.02545237932090.475570329499-22.8892192233-0.40858497134-10.462474378
54.91001042572.15283790755-0.7107417305254.081770637740.3980441328482.88408349451-0.1999114343760.668174025731-0.5876687575740.09410721329980.245350647371-0.153498228090.60516027606-0.46863254441-0.03545729663940.300382358119-0.07610254410860.02325857849550.430938195652-0.03994345502110.331812337171-39.2789825205-5.36799459517-10.2199940012
65.828764658743.511179339741.241450364126.06242979272.878750408023.65108096745-0.390770711537-0.5693856975571.02216415604-0.0496288048859-0.0873624584654-1.6994862886-2.755514449842.02325002024-0.6303802656250.672881664828-0.2447807290490.02823478826010.6961465360030.1022171749270.525145143469-33.3190966911.5162223296-3.54582236983
76.06343296608-0.235322547267-1.696419897535.93965606551-0.7607188397336.12136083441-0.02128319162430.333974642898-0.25434648887-0.013989383683-0.00928071439224-0.03954176711720.07767167467610.130336812158-0.02266788830120.157633379785-0.0135124519922-6.05382973183E-50.4044506388920.05360262084150.247703160011-37.199558468-0.350955816317-8.73426753187
86.715300054761.45458956321-0.413528703854.251832474371.606584881775.57232384707-0.5654237256520.911728839678-0.6561586182730.2767652775610.66313094368-0.0889238336731-0.0836845126132-0.1024791376450.3734345462210.1350387402590.06129679776170.01937284097670.36433068589-0.08303840747890.407534171908-43.0760590988-3.18448795319-7.47755076331
96.136230803212.534944649160.6508366197452.677020413841.65906767416.54674600356-0.3743164819780.0712927671310.167634268982-0.7873411138940.6784190863170.463551756361-0.6997362054960.139048710303-0.1054765044290.220770713157-0.006285441830860.02116241282770.3888039508370.05872921066870.357139805747-27.3200722964.23572295832-10.280838408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1000 through 1008 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1009 through 1079 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1080 through 1092 )
4X-RAY DIFFRACTION4chain 'C' and (resid 516 through 521 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1000 through 1020 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1021 through 1035 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1036 through 1079 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1080 through 1092 )
9X-RAY DIFFRACTION9chain 'D' and (resid 515 through 521 )

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