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- PDB-5heb: The third PDZ domain from the synaptic protein PSD-95 in complex ... -

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Basic information

Entry
Database: PDB / ID: 5heb
TitleThe third PDZ domain from the synaptic protein PSD-95 in complex with a C-terminal peptide derived from CRIPT
Components
  • Cysteine-rich PDZ-binding protein
  • Disks large homolog 4
KeywordsPEPTIDE BINDING PROTEIN / PDZ / GLGF / DHR / adhesion / synapse / synaptic density / peptide-binding domain
Function / homology
Function and homology information


regulation of postsynaptic density protein 95 clustering / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of postsynaptic density assembly / structural constituent of postsynaptic density ...regulation of postsynaptic density protein 95 clustering / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of postsynaptic density assembly / structural constituent of postsynaptic density / proximal dendrite / receptor localization to synapse / positive regulation of neuron projection arborization / protein localization to microtubule / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / frizzled binding / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / dendritic spine organization / acetylcholine receptor binding / positive regulation of synapse assembly / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / cortical cytoskeleton / regulation of neuronal synaptic plasticity / locomotory exploration behavior / postsynaptic density, intracellular component / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / kinesin binding / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of protein tyrosine kinase activity / positive regulation of synaptic transmission / cytoplasmic microtubule organization / ionotropic glutamate receptor binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / RNA splicing / dendritic shaft / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / spliceosomal complex / neuromuscular junction / establishment of protein localization / cell-cell adhesion / cerebral cortex development / mRNA processing / kinase binding / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynapse / microtubule binding / scaffold protein binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / neuronal cell body / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
PDZ-binding protein, CRIPT / Microtubule-associated protein CRIPT / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...PDZ-binding protein, CRIPT / Microtubule-associated protein CRIPT / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 4 / Cysteine-rich PDZ-binding protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWhite, K.I. / Raman, A.S. / Ranganathan, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationI-1366 United States
CitationJournal: Cell(Cambridge,Mass.) / Year: 2016
Title: Origins of Allostery and Evolvability in Proteins: A Case Study.
Authors: Raman, A.S. / White, K.I. / Ranganathan, R.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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: Disks large homolog 4
B: Cysteine-rich PDZ-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9924
Polymers13,8082
Non-polymers1842
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-5 kcal/mol
Surface area7020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.771, 89.771, 89.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

21A-713-

HOH

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Components

#1: Protein Disks large homolog 4 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP90


Mass: 12738.067 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31016
#2: Protein/peptide Cysteine-rich PDZ-binding protein / Cysteine-rich interactor of PDZ three / Cysteine-rich interactor of PDZ3


Mass: 1070.196 Da / Num. of mol.: 1 / Fragment: PDZ3-binding domain (UNP residues 93-101) / Source method: obtained synthetically
Details: Synthesized using standard FMOC chemistry, HPCL purified, and lyophilized.
Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q792Q4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein ...Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→40.147 Å / Num. obs: 15083 / % possible obs: 97.6 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 61.571
Reflection shellResolution: 1.65→1.703 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.478 / % possible all: 76

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2104refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BE9

1be9


Resolution: 1.65→40.147 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 1509 10.01 %random selection
Rwork0.1666 ---
obs0.1694 15082 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→40.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 12 122 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071125
X-RAY DIFFRACTIONf_angle_d1.221539
X-RAY DIFFRACTIONf_dihedral_angle_d21.811430
X-RAY DIFFRACTIONf_chiral_restr0.053167
X-RAY DIFFRACTIONf_plane_restr0.005216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70330.28731030.2255933X-RAY DIFFRACTION76
1.7033-1.76420.2341340.19481193X-RAY DIFFRACTION97
1.7642-1.83480.18871370.17491233X-RAY DIFFRACTION100
1.8348-1.91830.19941370.16551232X-RAY DIFFRACTION100
1.9183-2.01940.19731370.15851238X-RAY DIFFRACTION100
2.0194-2.14590.21121380.16431247X-RAY DIFFRACTION100
2.1459-2.31160.18551410.15931260X-RAY DIFFRACTION100
2.3116-2.54420.19451400.15981266X-RAY DIFFRACTION100
2.5442-2.91230.17961410.16511264X-RAY DIFFRACTION100
2.9123-3.66880.1761440.16211302X-RAY DIFFRACTION100
3.6688-40.15870.1981570.16751405X-RAY DIFFRACTION100
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)
11.62510.15190.00011.5332-0.39841.7641-0.01560.0116-0.02810.00960.1132-0.0168-0.1025-0.1697-0.07420.080.0001-0.00420.08670.0210.075340.023561.761332.9444
21.5392-0.87150.00122.5207-0.26552.0814-0.03640.00610.0080.06970.1268-0.08870.08730.0033-0.06460.0849-0.01430.00170.07430.01120.060743.679555.886534.8727
33.9162-0.1101-0.8861.3060.88555.33640.02870.1683-0.9001-0.0420.10050.41290.7499-0.2527-0.13010.2341-0.0605-0.03920.1903-0.03760.30539.089952.442322.646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 297:378)
2X-RAY DIFFRACTION2(chain A and resid 379:415)
3X-RAY DIFFRACTION3(chain B)

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