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- PDB-5wou: Crystal Structure of drosophila melanogaster Scribble PDZ1 domain... -

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Basic information

Entry
Database: PDB / ID: 5wou
TitleCrystal Structure of drosophila melanogaster Scribble PDZ1 domain in complex with Guk-Holder
Components
  • GUK-holder, isoform A
  • Protein lap4
KeywordsCELL ADHESION / Scribble / PDZ domain / Guk-holder / cell polarity
Function / homology
Function and homology information


Malpighian tubule development / RHOQ GTPase cycle / establishment of imaginal disc-derived wing hair orientation / establishment of ommatidial planar polarity / R3/R4 cell fate commitment / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / septate junction / septate junction assembly / negative regulation of imaginal disc growth ...Malpighian tubule development / RHOQ GTPase cycle / establishment of imaginal disc-derived wing hair orientation / establishment of ommatidial planar polarity / R3/R4 cell fate commitment / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / septate junction / septate junction assembly / negative regulation of imaginal disc growth / morphogenesis of follicular epithelium / establishment or maintenance of polarity of follicular epithelium / morphogenesis of larval imaginal disc epithelium / Unblocking of NMDA receptors, glutamate binding and activation / zonula adherens assembly / anterior/posterior axis specification, follicular epithelium / pole plasm protein localization / fusome / basal protein localization / establishment or maintenance of polarity of embryonic epithelium / dorsal closure / establishment or maintenance of apical/basal cell polarity / follicle cell of egg chamber development / basolateral part of cell / wing disc morphogenesis / compound eye development / neurotransmitter receptor transport postsynaptic membrane to endosome / olfactory behavior / morphogenesis of embryonic epithelium / morphogenesis of a polarized epithelium / Neutrophil degranulation / receptor localization to synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / apicolateral plasma membrane / establishment of epithelial cell apical/basal polarity / regulation of synapse structure or activity / establishment or maintenance of epithelial cell apical/basal polarity / cell fate specification / protein kinase A regulatory subunit binding / receptor clustering / regulation of endocytosis / lateral plasma membrane / bicellular tight junction / stem cell proliferation / stem cell differentiation / adherens junction / neuromuscular junction / cell morphogenesis / protein localization / terminal bouton / memory / cell-cell adhesion / negative regulation of epithelial cell proliferation / sensory perception of smell / cell junction / actin binding / cell cortex / actin cytoskeleton organization / basolateral plasma membrane / postsynaptic density / cytoskeleton / negative regulation of cell population proliferation / cytoplasm
Similarity search - Function
SCAR/WAVE family / 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. ...SCAR/WAVE family / 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
TRIETHYLENE GLYCOL / Protein lap4 / Wiskott-Aldrich syndrome protein family member
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCaria, S. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Drosophila melanogasterGuk-holder interacts with the Scribbled PDZ1 domain and regulates epithelial development with Scribbled and Discs Large.
Authors: Caria, S. / Magtoto, C.M. / Samiei, T. / Portela, M. / Lim, K.Y.B. / How, J.Y. / Stewart, B.Z. / Humbert, P.O. / Richardson, H.E. / Kvansakul, M.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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

Downloads & links

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Assembly

Deposited unit
A: Protein lap4
V: GUK-holder, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,87110
Polymers11,2862
Non-polymers5858
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.429, 53.884, 94.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

21A-242-

HOH

31A-277-

HOH

41A-326-

HOH

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Components

#1: Protein Protein lap4 / Protein scribble / Protein smell-impaired


Mass: 10408.926 Da / Num. of mol.: 1 / Fragment: PDZ1 domain (UNP residues 726-820)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: scrib, smi, vart, CG5462 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q7KRY7
#2: Protein/peptide GUK-holder, isoform A


Mass: 876.993 Da / Num. of mol.: 1 / Fragment: UNP residues 1781-1788 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VE13
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % (v/v) PEG 4000, 0.2 M sodium acetate and 0.1M Tris chloride pH 8.5

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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 315r / Detector: CCD / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→31.42 Å / Num. obs: 13578 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Biso Wilson estimate: 11.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.031 / Net I/σ(I): 18.4
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 617 / CC1/2: 0.92 / Rpim(I) all: 0.23 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWC

5vwc


Resolution: 1.55→30.179 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 684 5.05 %
Rwork0.1967 --
obs0.1981 13548 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→30.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 38 134 931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003815
X-RAY DIFFRACTIONf_angle_d0.681087
X-RAY DIFFRACTIONf_dihedral_angle_d16.88485
X-RAY DIFFRACTIONf_chiral_restr0.053129
X-RAY DIFFRACTIONf_plane_restr0.004139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5495-1.66920.28961470.23362448X-RAY DIFFRACTION96
1.6692-1.83710.22781360.20742545X-RAY DIFFRACTION97
1.8371-2.10290.23511400.1912541X-RAY DIFFRACTION98
2.1029-2.64920.22391280.1962604X-RAY DIFFRACTION98
2.6492-30.18520.20261330.18952726X-RAY DIFFRACTION99
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)
10.22830.01850.24520.2290.09820.61770.0520.0546-0.15040.00580.0123-0.05690.16710.0709-0.04080.0874-0.00360.02010.0381-0.01360.148220.690611.424335.553
20.0414-0.06270.02220.1586-0.00250.04720.01650.10140.01470.0246-0.0452-0.02390.0138-0.0147-0.0080.0670.00990.00720.0873-0.02530.07117.441225.611731.4837
30.0593-0.03850.02290.0314-0.00510.00240.00770.00730.01990.0319-0.0099-0.0647-0.06960.0408-0.00610.0759-0.00390.00710.0903-0.00860.074624.345918.277431.7183
40.0104-0.0036-0.00290.03510.00750.0138-0.0133-0.0029-0.01130.06150.06040.12480.0662-0.0488-0.00130.0819-0.00730.00580.08960.00660.075616.035123.813743.4805
50.1038-0.01-0.04870.00180.01220.0605-0.0231-0.10490.1397-0.00430.014-0.03710.00520.1248-0.00280.1020.00850.01240.0682-0.0150.071722.940329.781541.179
60.0419-0.0913-0.00480.3286-0.10360.12540.1194-0.012-0.14020.15150.06710.16520.0512-0.08650.10590.0874-0.01140.00360.0818-0.0240.081819.541514.217834.7614
70.0612-0.06620.04070.1537-0.11140.0834-0.0656-0.0375-0.01090.0903-0.07670.05560.0674-0.0658-0.0120.09690.00830.00070.1031-0.0270.086617.33232.926930.8262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 70 )
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 83 )
6X-RAY DIFFRACTION6chain 'A' and (resid 84 through 94 )
7X-RAY DIFFRACTION7chain 'V' and (resid 98 through 105 )

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