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- PDB-6xa8: Crystal Structure of Human Scribble PDZ1:Vangl2 complex -

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Basic information

Entry
Database: PDB / ID: 6xa8
TitleCrystal Structure of Human Scribble PDZ1:Vangl2 complex
Components
  • C-terminal peptide of Vangl2
  • Protein scribble homolog
KeywordsCYTOSOLIC PROTEIN / Cell polarity / Scribble
Function / homology
Function and homology information


apoptotic process involved in morphogenesis / : / establishment of T cell polarity / polarized epithelial cell differentiation / establishment of apical/basal cell polarity / mammary gland duct morphogenesis / epithelial structure maintenance / Scrib-APC-beta-catenin complex / neurotransmitter receptor transport, endosome to postsynaptic membrane / activation of GTPase activity ...apoptotic process involved in morphogenesis / : / establishment of T cell polarity / polarized epithelial cell differentiation / establishment of apical/basal cell polarity / mammary gland duct morphogenesis / epithelial structure maintenance / Scrib-APC-beta-catenin complex / neurotransmitter receptor transport, endosome to postsynaptic membrane / activation of GTPase activity / myelin sheath abaxonal region / establishment or maintenance of epithelial cell apical/basal polarity / cell-cell contact zone / negative regulation of mitotic cell cycle / protein localization to adherens junction / RND2 GTPase cycle / RND3 GTPase cycle / negative regulation of activated T cell proliferation / neural tube closure / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / positive regulation of receptor recycling / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / signaling adaptor activity / adherens junction / cell-cell adhesion / Asymmetric localization of PCP proteins / positive regulation of type II interferon production / cell junction / cell population proliferation / cell-cell junction / cell migration / lamellipodium / presynapse / basolateral plasma membrane / postsynaptic density / positive regulation of apoptotic process / cadherin binding / protein kinase binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / PDZ domain profile. ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
A: Protein scribble homolog
B: Protein scribble homolog
C: C-terminal peptide of Vangl2
D: C-terminal peptide of Vangl2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,67611
Polymers27,1104
Non-polymers5667
Water19811
1
A: Protein scribble homolog
D: C-terminal peptide of Vangl2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8075
Polymers13,5552
Non-polymers2523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-13 kcal/mol
Surface area6520 Å2
MethodPISA
2
B: Protein scribble homolog
C: C-terminal peptide of Vangl2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8696
Polymers13,5552
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-11 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.379, 75.379, 212.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11B-1104-

HOH

21C-501-

HOH

31D-401-

HOH

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Components

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


Mass: 12792.356 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 C-terminal peptide of Vangl2


Mass: 762.806 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Phosphate/citrate pH 4.2 and 40% (v/v) PEG 300

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9357 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9357 Å / Relative weight: 1
ReflectionResolution: 2.2→51.703 Å / Num. obs: 15662 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 51.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.4
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1349 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MS1

6ms1


Resolution: 2.2→51.7 Å / SU ML: 0.2768 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 35.2871
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2691 778 4.99 %
Rwork0.2585 14828 -
obs0.2591 15606 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→51.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 28 11 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261625
X-RAY DIFFRACTIONf_angle_d0.52182190
X-RAY DIFFRACTIONf_chiral_restr0.0476250
X-RAY DIFFRACTIONf_plane_restr0.0029290
X-RAY DIFFRACTIONf_dihedral_angle_d30.1926589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.32831290.34772464X-RAY DIFFRACTION99.46
2.34-2.520.34341140.31552440X-RAY DIFFRACTION99.53
2.52-2.770.38131360.29962446X-RAY DIFFRACTION99.38
2.77-3.170.35271230.31752433X-RAY DIFFRACTION99.88
3.17-40.2811340.26342486X-RAY DIFFRACTION99.81
4-51.70.2191420.22132559X-RAY DIFFRACTION99.7

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