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- PDB-3hpk: Oxidized dimeric PICK1 PDZ in complex with the carboxyl tail pept... -

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Basic information

Entry
Database: PDB / ID: 3hpk
TitleOxidized dimeric PICK1 PDZ in complex with the carboxyl tail peptide of GluR2
ComponentsPRKCA-binding protein,9-mer peptide of THE GLUR2 SUBUNIT
KeywordsPROTEIN BINDING / oxidized / PDZ domain / Kinase
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic endocytic zone / postsynaptic early endosome / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation ...G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic endocytic zone / postsynaptic early endosome / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / monoamine transport / dopamine transport / SNAP receptor activity / protein kinase C-activating G protein-coupled receptor signaling pathway / dendritic spine organization / regulation of postsynaptic neurotransmitter receptor internalization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / Trafficking of GluR2-containing AMPA receptors / regulation of insulin secretion / positive regulation of receptor internalization / protein targeting / cellular response to glucose starvation / ionotropic glutamate receptor binding / cytoskeletal protein binding / ephrin receptor binding / protein kinase C binding / trans-Golgi network membrane / G protein-coupled receptor binding / phospholipid binding / intracellular protein transport / receptor tyrosine kinase binding / actin filament binding / synaptic vesicle / GTPase binding / presynaptic membrane / actin binding / dendritic spine / postsynaptic density / cytoskeleton / neuron projection / protein domain specific binding / negative regulation of gene expression / signaling receptor binding / protein phosphorylation / intracellular membrane-bounded organelle / dendrite / glutamatergic synapse / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / mitochondrion / membrane / identical protein binding / metal ion binding / plasma membrane / 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 / PRKCA-binding protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYu, J. / Shi, Y. / Zhang, M.
CitationJournal: Biochemistry / Year: 2010
Title: Redox-Regulated Lipid Membrane Binding of the PICK1 PDZ Domain.
Authors: Shi, Y. / Yu, J. / Jia, Y. / Pan, L. / Shen, C. / Xia, J. / Zhang, M.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref
Item: _entity.pdbx_description / _entity_name_com.name / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRKCA-binding protein,9-mer peptide of THE GLUR2 SUBUNIT
B: PRKCA-binding protein,9-mer peptide of THE GLUR2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8713
Polymers26,7792
Non-polymers921
Water2,378132
1
A: PRKCA-binding protein,9-mer peptide of THE GLUR2 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)13,3891
Polymers13,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PRKCA-binding protein,9-mer peptide of THE GLUR2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4812
Polymers13,3891
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-16 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.260, 51.790, 80.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PRKCA-binding protein,9-mer peptide of THE GLUR2 SUBUNIT / Protein interacting with C kinase 1 / isoform CRA_b / Protein interacting with PRKCA 1


Mass: 13389.304 Da / Num. of mol.: 2 / Fragment: PICK1 PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) synthetic construct (others)
Gene: Pick1, rCG_60080 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GQQ2, UniProt: Q9EP80*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS FUSED WITH PROTEASE 3C CLEAVAGE SITE AND THE C-TERMINAL TAIL 9 AMINO ACID RESIDUES ...THIS SEQUENCE IS FUSED WITH PROTEASE 3C CLEAVAGE SITE AND THE C-TERMINAL TAIL 9 AMINO ACID RESIDUES OF THE GLUR2 SUBUNIT.

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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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 20% (w/v) PEG3350, 0.2M Lithium Citrate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→80.85 Å / Num. all: 11020 / Num. obs: 11020 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 36.778 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1571 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PKU

2pku


Resolution: 2.2→80.85 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.059 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23463 1082 9.8 %RANDOM
Rwork0.20565 ---
obs0.20848 9933 99.81 %-
all-11020 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→80.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 6 132 1760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221650
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.992234
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15427.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66415295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.215152
X-RAY DIFFRACTIONr_chiral_restr0.0680.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021202
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2725
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21155
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.51116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85321744
X-RAY DIFFRACTIONr_scbond_it1.1783593
X-RAY DIFFRACTIONr_scangle_it1.884.5490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 81 -
Rwork0.222 728 -
obs--99.39 %
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)
13.08170.8072-1.07183.3118-0.89522.84570.08990.16810.0461-0.0645-0.05090.24160.0173-0.1403-0.0389-0.102-0.0010.0103-0.0815-0.0302-0.0821-14.2023-1.2475-17.9041
22.11051.09330.80685.01922.40086.02190.0197-0.0011-0.05640.2258-0.07290.070.3271-0.08630.0532-0.1066-0.030.0034-0.082-0.0088-0.1075-1.814418.3286-7.0059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 125
2X-RAY DIFFRACTION2B19 - 125

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