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- PDB-6xa7: Crystal Structure of Human Scribble PDZ2:Vangl2 complex -

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Basic information

Entry
Database: PDB / ID: 6xa7
TitleCrystal Structure of Human Scribble PDZ2:Vangl2 complex
Components
  • Protein scribble homolog
  • Vang-like protein 2
KeywordsCYTOSOLIC PROTEIN / Cell polarity / Scribble
Function / homology
Function and homology information


cell migration involved in kidney development / dopaminergic neuron axon guidance / serotonergic neuron axon guidance / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / establishment of planar polarity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development ...cell migration involved in kidney development / dopaminergic neuron axon guidance / serotonergic neuron axon guidance / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / establishment of planar polarity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / Scrib-APC-beta-catenin complex / astrocyte cell migration / synaptic vesicle targeting / polarized epithelial cell differentiation / epithelial structure maintenance / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / apical protein localization / post-anal tail morphogenesis / non-motile cilium assembly / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / PCP/CE pathway / auditory receptor cell stereocilium organization / regulation of postsynaptic neurotransmitter receptor internalization / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle / RND3 GTPase cycle / receptor clustering / positive chemotaxis / positive regulation of receptor recycling / heart looping / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / negative regulation of mitotic cell cycle / immunological synapse / synaptic vesicle endocytosis / lateral plasma membrane / signaling adaptor activity / neural tube closure / Asymmetric localization of PCP proteins / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / cell junction / lamellipodium / presynapse / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / apical plasma membrane / glutamatergic synapse / protein kinase binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Vang-like protein / Strabismus protein / : / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain ...Vang-like protein / Strabismus protein / : / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / 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
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: 2.5 Å
AuthorsHow, J.Y. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1079133 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 1.2Apr 3, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,20615
Polymers42,7728
Non-polymers4347
Water2,378132
1
A: Protein scribble homolog
E: Vang-like protein 2


Theoretical massNumber of molelcules
Total (without water)10,6932
Polymers10,6932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein scribble homolog
F: Vang-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8174
Polymers10,6932
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein scribble homolog
G: Vang-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9416
Polymers10,6932
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein scribble homolog
H: Vang-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7553
Polymers10,6932
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.047, 60.765, 96.017
Angle α, β, γ (deg.)90.000, 106.481, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)

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Components

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


Mass: 9772.996 Da / Num. of mol.: 4
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.: 4 / Fragment: C-terminal residues 514-521 / 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.: 7 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium thiocyanate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→47.174 Å / Num. obs: 13826 / % possible obs: 91.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 30.84 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1396 / CC1/2: 0.856 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDZ3-Vangl2

Resolution: 2.5→47.17 Å / SU ML: 0.3466 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2672 661 4.79 %
Rwork0.2362 13151 -
obs0.2377 13812 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 28 132 2946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832838
X-RAY DIFFRACTIONf_angle_d0.98213822
X-RAY DIFFRACTIONf_chiral_restr0.0517456
X-RAY DIFFRACTIONf_plane_restr0.0054503
X-RAY DIFFRACTIONf_dihedral_angle_d34.2551434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.37751350.31882680X-RAY DIFFRACTION94.15
2.69-2.960.29561140.28082706X-RAY DIFFRACTION94.41
2.96-3.390.34051350.25812660X-RAY DIFFRACTION92.37
3.39-4.270.23051360.20482540X-RAY DIFFRACTION89.17
4.27-47.170.21851410.2022565X-RAY DIFFRACTION87.6

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