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- PDB-1rzx: Crystal Structure of a Par-6 PDZ-peptide Complex -

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Basic information

Entry
Database: PDB / ID: 1rzx
TitleCrystal Structure of a Par-6 PDZ-peptide Complex
Components
  • Acetylated VKESLV Peptide
  • CG5884-PA
KeywordsCELL CYCLE
Function / homology
Function and homology information


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 ...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 / asymmetric neuroblast division / morphogenesis of a polarized epithelium / apical cortex / 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 / terminal bouton / cell cortex / apical plasma membrane / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPeterson, F.C. / Penkert, R.R. / Volkman, F.B. / Prehoda, K.E.
CitationJournal: Mol.Cell / Year: 2004
Title: Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition.
Authors: Peterson, F.C. / Penkert, R.R. / Volkman, B.F. / Prehoda, K.E.
History
DepositionDec 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG5884-PA
B: Acetylated VKESLV Peptide


Theoretical massNumber of molelcules
Total (without water)11,1982
Polymers11,1982
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.853, 64.853, 52.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-8-

HOH

21A-15-

HOH

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Components

#1: Protein CG5884-PA / Par-6


Mass: 10497.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: par-6 / Plasmid: pBH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O97111
#2: Protein/peptide Acetylated VKESLV Peptide


Mass: 700.844 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This protein was chemically synthesized. The N-terminal has been acetylated (ACE)VKESLV.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 26% PEG6000, 100 mM HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 %PEG60001reservoir
2100 mMHEPES1reservoirpH7.1
310 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 7402 / Num. obs: 7357 / % possible obs: 99.4 %
Reflection shellResolution: 2.1→2.18 Å / % possible all: 96
Reflection
*PLUS
Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 96.1 % / Num. unique obs: 693 / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 10.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nf3

1nf3


Resolution: 2.1→30 Å
RfactorNum. reflectionSelection details
Rfree0.27 368 random
Rwork0.22 --
all0.22 7357 -
obs0.22 7357 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 0 45 831
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.005
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.06

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