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- PDB-2gzv: The cystal structure of the PDZ domain of human PICK1 -

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Basic information

Entry
Database: PDB / ID: 2gzv
TitleThe cystal structure of the PDZ domain of human PICK1
ComponentsPRKCA-binding protein
KeywordsSIGNALING PROTEIN / protein kinase C / PDZ domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


membrane curvature sensor activity / postsynaptic early endosome / glial cell development / neuronal ion channel clustering / cellular response to decreased oxygen levels / Arp2/3 complex binding / Trafficking of GluR2-containing AMPA receptors / epigenetic programming of gene expression / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation ...membrane curvature sensor activity / postsynaptic early endosome / glial cell development / neuronal ion channel clustering / cellular response to decreased oxygen levels / Arp2/3 complex binding / Trafficking of GluR2-containing AMPA receptors / epigenetic programming of gene expression / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / monoamine transport / genomic imprinting / protein kinase C-activating G protein-coupled receptor signaling pathway / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / dendritic spine organization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / positive regulation of receptor internalization / regulation of insulin secretion / cellular response to glucose starvation / protein kinase C binding / trans-Golgi network membrane / G protein-coupled receptor binding / Cell surface interactions at the vascular wall / phospholipid binding / intracellular protein transport / endocytic vesicle membrane / actin filament binding / synaptic vesicle / presynaptic membrane / postsynaptic density / cytoskeleton / neuron projection / protein domain specific binding / signaling receptor binding / protein phosphorylation / synapse / perinuclear region of cytoplasm / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain ...PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / 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
PRKCA-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsDebreczeni, J.E. / Elkins, J.M. / Yang, X. / Berridge, G. / Bray, J. / Colebrook, S. / Smee, C. / Savitsky, P. / Gileadi, O. / Turnbull, A. ...Debreczeni, J.E. / Elkins, J.M. / Yang, X. / Berridge, G. / Bray, J. / Colebrook, S. / Smee, C. / Savitsky, P. / Gileadi, O. / Turnbull, A. / von Delft, F. / Doyle, D.A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.
Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A.
History
DepositionMay 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Structure summary / Category: software / struct
Item: _software.classification / _software.name / _struct.title
Revision 1.4Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRKCA-binding protein


Theoretical massNumber of molelcules
Total (without water)12,4271
Polymers12,4271
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PRKCA-binding protein

A: PRKCA-binding protein


Theoretical massNumber of molelcules
Total (without water)24,8542
Polymers24,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2470 Å2
ΔGint-21 kcal/mol
Surface area9690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.588, 37.257, 29.442
Angle α, β, γ (deg.)90.00, 95.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-168-

HOH

21A-210-

HOH

31A-212-

HOH

DetailsThe monomer present in the asymmetric unit is the biological unit.

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Components

#1: Protein PRKCA-binding protein / Protein kinase C-alpha-binding protein / Protein interacting with C kinase 1


Mass: 12427.161 Da / Num. of mol.: 1 / Fragment: PDZ domain, residues 19-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PICK1, PRKCABP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3/Rosetta / References: UniProt: Q9NRD5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.75 Å3/Da / Density % sol: 29.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium-acetate, 0.1 M Bis-Tris, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97925 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.12→29.3 Å / Num. all: 33346 / Num. obs: 32802 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0565
Reflection shellResolution: 1.12→1.22 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.0126 / Mean I/σ(I) obs: 7.97 / Num. unique all: 7289 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FNE

2fne


Resolution: 1.12→29.3 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.795 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16865 1659 5.1 %RANDOM
Rwork0.14911 ---
all0.15007 33346 --
obs0.15007 31143 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.11 Å2
2---0.03 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.12→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms667 0 0 144 811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022741
X-RAY DIFFRACTIONr_bond_other_d0.0010.02485
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9751018
X-RAY DIFFRACTIONr_angle_other_deg0.87831219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72926.66727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.15715134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.812151
X-RAY DIFFRACTIONr_chiral_restr0.0810.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02127
X-RAY DIFFRACTIONr_nbd_refined0.2110.2164
X-RAY DIFFRACTIONr_nbd_other0.1740.2489
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2375
X-RAY DIFFRACTIONr_nbtor_other0.0920.2384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.223
X-RAY DIFFRACTIONr_mcbond_it3.0195514
X-RAY DIFFRACTIONr_mcbond_other2.4455201
X-RAY DIFFRACTIONr_mcangle_it3.6087787
X-RAY DIFFRACTIONr_scbond_it4.3569284
X-RAY DIFFRACTIONr_scangle_it5.44912222
X-RAY DIFFRACTIONr_rigid_bond_restr2.70231336
X-RAY DIFFRACTIONr_sphericity_free6.723144
X-RAY DIFFRACTIONr_sphericity_bonded4.63231207
LS refinement shellResolution: 1.118→1.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 97 -
Rwork0.209 2091 -
obs--90.34 %

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