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- PDB-5hfb: The third PDZ domain from the synaptic protein PSD-95 (H372A muta... -

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Basic information

Entry
Database: PDB / ID: 5hfb
TitleThe third PDZ domain from the synaptic protein PSD-95 (H372A mutant) 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 / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of postsynaptic density assembly / receptor localization to synapse ...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 / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of postsynaptic density assembly / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / proximal dendrite / protein localization to microtubule / AMPA glutamate receptor clustering / cerebellar mossy fiber / protein localization to synapse / cellular response to potassium ion / vocalization behavior / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / dendritic branch / Activation of Ca-permeable Kainate Receptor / juxtaparanode region of axon / neuron projection terminus / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / frizzled binding / 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 / regulation of neuronal synaptic plasticity / locomotory exploration behavior / cortical cytoskeleton / postsynaptic density, intracellular component / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / kinesin binding / 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 / spliceosomal complex / regulation of long-term neuronal synaptic plasticity / 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 / microtubule binding / postsynaptic membrane / postsynapse / scaffold protein binding / basolateral plasma membrane / protein-containing complex assembly / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / dendrite / neuronal cell body / glutamatergic synapse / 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: 1.616 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 6, 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)13,7412
Polymers13,7412
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-3 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.592, 89.592, 89.592
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-610-

HOH

21A-637-

HOH

31B-104-

HOH

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Components

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


Mass: 12670.998 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402) / Mutation: H372A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
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 1.2 M sodium citrate, pH 7.0. 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 1.2 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (8 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 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.616→40.067 Å / Num. obs: 15110 / % possible obs: 92.53 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 65.515
Reflection shellRedundancy: 1.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 0.936

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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: 1.616→40.067 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1513 10.01 %random selection
Rwork0.1751 ---
obs0.178 15110 92.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.616→40.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 148 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061082
X-RAY DIFFRACTIONf_angle_d0.9451487
X-RAY DIFFRACTIONf_dihedral_angle_d23.284410
X-RAY DIFFRACTIONf_chiral_restr0.048166
X-RAY DIFFRACTIONf_plane_restr0.004209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6159-1.66810.3207450.311409X-RAY DIFFRACTION31
1.6681-1.72770.23961240.23941116X-RAY DIFFRACTION86
1.7277-1.79690.241410.19151266X-RAY DIFFRACTION99
1.7969-1.87860.20251460.17311315X-RAY DIFFRACTION100
1.8786-1.97770.22131460.19921318X-RAY DIFFRACTION100
1.9777-2.10160.21491470.18431311X-RAY DIFFRACTION100
2.1016-2.26380.21921470.16991326X-RAY DIFFRACTION100
2.2638-2.49160.17691490.16371342X-RAY DIFFRACTION100
2.4916-2.85210.20251490.16231337X-RAY DIFFRACTION100
2.8521-3.5930.2231530.16111378X-RAY DIFFRACTION100
3.593-40.07910.17431660.17441479X-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)
12.01630.7956-0.42931.92950.6652.02430.0546-0.11370.09960.1458-0.0554-0.4865-0.2030.3470.03050.146-0.0224-0.01570.1620.03480.188146.49665.89641.9586
23.3344-1.8774-0.38362.6993-1.34753.5926-0.08540.2798-0.121-0.19470.07880.12520.3329-0.40090.03360.107-0.0509-0.030.14450.01340.069237.978558.384927.0758
31.7427-0.0687-1.00421.531-0.8141.71830.02010.26760.1265-0.07280.11470.0776-0.0681-0.2991-0.07050.081-0.0054-0.01510.11980.02950.075737.033861.89730.6361
42.1115-1.3477-0.17462.6284-0.20412.6713-0.11580.01450.00880.11450.1793-0.10860.13570.0385-0.01980.0866-0.0135-0.0020.06790.00610.078845.162455.013735.9402
54.968-4.96610.73685.0098-0.43052.1806-0.07590.3272-0.6698-0.1651-0.15141.07640.83380.06320.2020.3725-0.01750.03070.279-0.02370.372339.118955.039122.5668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 299:319)
2X-RAY DIFFRACTION2(chain A and resid 320:339)
3X-RAY DIFFRACTION3(chain A and resid 340:381)
4X-RAY DIFFRACTION4(chain A and resid 382:415)
5X-RAY DIFFRACTION5(chain B and resid 4:9)

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