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- PDB-5vwk: Crystal structure of human Scribble PDZ1:Beta-PIX complex -

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Basic information

Entry
Database: PDB / ID: 5vwk
TitleCrystal structure of human Scribble PDZ1:Beta-PIX complex
Components
  • Beta-PIX
  • Protein scribble homolog
KeywordsSTRUCTURAL PROTEIN / polarity
Function / homology
Function and homology information


extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / protein localization to adherens junction / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / lamellipodium / cell junction / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
Leucine Rich Repeat / 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 ...Leucine Rich Repeat / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLim, K.Y.B. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1007918 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis for the differential interaction of Scribble PDZ domains with the guanine nucleotide exchange factor beta-PIX.
Authors: Lim, K.Y.B. / Godde, N.J. / Humbert, P.O. / Kvansakul, M.
History
DepositionMay 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 scribble homolog
B: Protein scribble homolog
C: Protein scribble homolog
D: Protein scribble homolog
E: Beta-PIX
F: Beta-PIX
G: Beta-PIX
H: Beta-PIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,10220
Polymers54,9498
Non-polymers1,15312
Water4,432246
1
A: Protein scribble homolog
H: Beta-PIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0265
Polymers13,7372
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-53 kcal/mol
Surface area6900 Å2
MethodPISA
2
B: Protein scribble homolog
G: Beta-PIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9294
Polymers13,7372
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-51 kcal/mol
Surface area6830 Å2
MethodPISA
3
C: Protein scribble homolog
F: Beta-PIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1226
Polymers13,7372
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-25 kcal/mol
Surface area6930 Å2
MethodPISA
4
D: Protein scribble homolog
E: Beta-PIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0265
Polymers13,7372
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-24 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.760, 74.760, 222.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 12792.356 Da / Num. of mol.: 4 / Fragment: residues 700-816
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 K-12 (bacteria) / References: UniProt: Q14160
#2: Protein/peptide
Beta-PIX


Mass: 944.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.09
Details: 1.09M lithium sulfate and 0.1M trisodium citrate-citric acid pH5.09

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→47.77 Å / Num. obs: 26459 / % possible obs: 97.5 % / Redundancy: 4.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.738 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W4F

2w4f


Resolution: 2.35→38.357 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.94
RfactorNum. reflection% reflection
Rfree0.2565 1294 4.9 %
Rwork0.2229 --
obs0.2245 26411 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→38.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 60 246 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043379
X-RAY DIFFRACTIONf_angle_d0.6564566
X-RAY DIFFRACTIONf_dihedral_angle_d19.4821996
X-RAY DIFFRACTIONf_chiral_restr0.048504
X-RAY DIFFRACTIONf_plane_restr0.004600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.44410.33951410.29842787X-RAY DIFFRACTION99
2.4441-2.55530.31081500.27942766X-RAY DIFFRACTION99
2.5553-2.690.30031470.26612775X-RAY DIFFRACTION98
2.69-2.85850.28281640.25022770X-RAY DIFFRACTION98
2.8585-3.07910.26191270.23892791X-RAY DIFFRACTION98
3.0791-3.38880.25331230.21862799X-RAY DIFFRACTION97
3.3888-3.87870.22091440.20022799X-RAY DIFFRACTION97
3.8787-4.88520.19551380.17532797X-RAY DIFFRACTION95
4.8852-38.3620.28351600.21772833X-RAY DIFFRACTION91

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