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- PDB-5i7z: Crystal structure of a Par-6 PDZ-Crumbs 3 C-terminal peptide complex -

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Basic information

Entry
Database: PDB / ID: 5i7z
TitleCrystal structure of a Par-6 PDZ-Crumbs 3 C-terminal peptide complex
Components
  • Crb-3
  • LD29223p
KeywordsSIGNALING PROTEIN / PDZ / cell polarity
Function / homology
Function and homology information


positive regulation of cell junction assembly / CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / establishment of neuroblast polarity ...positive regulation of cell junction assembly / CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / establishment of neuroblast polarity / RHOU GTPase cycle / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Asymmetric localization of PCP proteins / establishment or maintenance of polarity of embryonic epithelium / muscle cell postsynaptic specialization / border follicle cell migration / Tight junction interactions / asymmetric neuroblast division / morphogenesis of a polarized epithelium / apical cortex / bicellular tight junction assembly / apical protein localization / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of smoothened signaling pathway / centrosome cycle / positive regulation of filopodium assembly / protein kinase inhibitor activity / bicellular tight junction / positive regulation of lamellipodium assembly / synapse assembly / protein localization to plasma membrane / terminal bouton / SH3 domain binding / cell junction / cell cortex / membrane => GO:0016020 / apical plasma membrane / protein domain specific binding / protein-containing complex / extracellular exosome / plasma membrane
Similarity search - Function
Partitioning defective protein 6, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Partitioning defective protein 6, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / LD29223p / Protein crumbs homolog 3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.801 Å
AuthorsWhitney, D.S. / Peterson, F.C. / Prehoda, K.E. / Volkman, B.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI058072 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM068032 United States
CitationJournal: Biochemistry / Year: 2016
Title: Binding of Crumbs to the Par-6 CRIB-PDZ Module Is Regulated by Cdc42.
Authors: Whitney, D.S. / Peterson, F.C. / Kittell, A.W. / Egner, J.M. / Prehoda, K.E. / Volkman, B.F.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: LD29223p
B: Crb-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3403
Polymers11,2342
Non-polymers1061
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-5 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.060, 65.060, 52.596
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

21A-456-

HOH

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Components

#1: Protein LD29223p / PAR-6 / Par-6 / isoform A / isoform B


Mass: 10266.793 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 158-253)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: par-6, CG5884, Dmel_CG5884 / Plasmid: PBH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O97111
#2: Protein/peptide Crb-3


Mass: 967.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BUF7*PLUS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 26% PEG 6000, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 10639 / % possible obs: 95.6 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 43.4
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.9 / % possible all: 70.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.801→38.448 Å / FOM work R set: 0.7847 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1058 9.94 %
Rwork0.1965 9581 -
obs0.1987 10639 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.85 Å2 / Biso mean: 37.11 Å2 / Biso min: 16.9 Å2
Refinement stepCycle: final / Resolution: 1.801→38.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 7 60 847
Biso mean--40.27 34.7 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015809
X-RAY DIFFRACTIONf_angle_d1.3241094
X-RAY DIFFRACTIONf_chiral_restr0.095131
X-RAY DIFFRACTIONf_plane_restr0.011143
X-RAY DIFFRACTIONf_dihedral_angle_d14.585312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.801-1.8830.3201790.273173781656
1.883-1.98230.30551080.25211043115178
1.9823-2.10640.27281340.22661223135792
2.1064-2.26910.25411370.20241275141296
2.2691-2.49740.24311480.20941315146399
2.4974-2.85860.23521500.21781292144298
2.8586-3.60120.22111520.196413321484100
3.6012-38.45640.1751500.169713641514100

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