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

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Basic information

Entry
Database: PDB / ID: 5hed
TitleThe third PDZ domain from the synaptic protein PSD-95 in complex with a mutant C-terminal peptide derived from CRIPT (T-2F)
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


RHO GTPases activate CIT / regulation of postsynaptic density protein 95 clustering / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density ...RHO GTPases activate CIT / regulation of postsynaptic density protein 95 clustering / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density / protein localization to microtubule / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / neuron spine / cerebellar mossy fiber / regulation of postsynaptic density assembly / AMPA glutamate receptor clustering / protein localization to synapse / positive regulation of dendrite morphogenesis / proximal dendrite / Trafficking of AMPA receptors / dendritic branch / LGI-ADAM interactions / Activation of Ca-permeable Kainate Receptor / dendritic spine morphogenesis / negative regulation of receptor internalization / frizzled binding / neuron projection terminus / acetylcholine receptor binding / juxtaparanode region of axon / regulation of NMDA receptor activity / dendritic spine organization / cellular response to potassium ion / RAF/MAP kinase cascade / positive regulation of synapse assembly / beta-2 adrenergic receptor binding / NMDA selective glutamate receptor signaling pathway / Synaptic adhesion-like molecules / neuromuscular process controlling balance / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / AMPA glutamate receptor complex / excitatory synapse / social behavior / regulation of neuronal synaptic plasticity / kinesin binding / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / D1 dopamine receptor binding / postsynaptic density, intracellular component / regulation of postsynaptic membrane neurotransmitter receptor levels / cytoplasmic microtubule organization / ionotropic glutamate receptor binding / dendrite cytoplasm / RNA splicing / synaptic membrane / dendritic shaft / cell periphery / PDZ domain binding / neuromuscular junction / spliceosomal complex / establishment of protein localization / cell-cell adhesion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / cerebral cortex development / kinase binding / mRNA processing / synaptic vesicle / cell-cell junction / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / microtubule binding / dendritic spine / chemical synaptic transmission / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol
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 ...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: 1.7 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, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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


Theoretical massNumber of molelcules
Total (without water)13,8542
Polymers13,8542
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-4 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.551, 89.551, 89.551
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-645-

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) / Mutation: T-2F
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: 1116.266 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.125 M sodium citrate, pH 7.1. Equal amounts (1.5 microliters) of ...Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.125 M sodium citrate, pH 7.1. 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: 100 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: 1.7→36.559 Å / Num. obs: 13974 / % possible obs: 99.25 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 60.017
Reflection shellResolution: 1.6997→1.7604 Å / Redundancy: 3 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.627

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Processing

Software
NameVersionClassification
PHENIXdev_2026refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BE9

1be9


Resolution: 1.7→36.559 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 17.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 1398 10 %random selection
Rwork0.1701 ---
obs0.1728 13974 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 0 152 1114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141137
X-RAY DIFFRACTIONf_angle_d1.461554
X-RAY DIFFRACTIONf_dihedral_angle_d14.712435
X-RAY DIFFRACTIONf_chiral_restr0.074165
X-RAY DIFFRACTIONf_plane_restr0.008222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6997-1.76040.27181280.22871156X-RAY DIFFRACTION94
1.7604-1.83090.25491370.19731228X-RAY DIFFRACTION99
1.8309-1.91420.251360.18461228X-RAY DIFFRACTION100
1.9142-2.01510.18551380.17411229X-RAY DIFFRACTION100
2.0151-2.14140.21691380.1671250X-RAY DIFFRACTION100
2.1414-2.30670.181400.16791256X-RAY DIFFRACTION100
2.3067-2.53870.19341400.15471260X-RAY DIFFRACTION100
2.5387-2.9060.17841420.15571274X-RAY DIFFRACTION100
2.906-3.66070.17691430.16291292X-RAY DIFFRACTION100
3.6607-36.56750.19551560.17431403X-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)
11.58950.0651-0.50371.6104-0.24231.8620.00060.0265-0.03050.03520.0366-0.0659-0.0452-0.0995-0.06070.08130.0017-0.0040.07590.01480.073239.46860.905133.1376
21.6029-0.9887-0.2641.6821-0.11871.8132-0.0354-0.0120.00260.03570.0812-0.07390.0733-0.007-0.0350.0776-0.0020.00630.06430.01490.084343.729855.782534.9958
31.53260.1430.16893.57-1.06812.08550.04120.2457-0.7475-0.29530.32350.6330.8726-0.1593-0.07560.3546-0.0276-0.01910.2185-0.01530.437238.290652.371622.7242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 298:378)
2X-RAY DIFFRACTION2(chain A and resid 379:415)
3X-RAY DIFFRACTION3(chain B)

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