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

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Basic information

Entry
Database: PDB / ID: 5hfc
TitleThe third PDZ domain from the synaptic protein PSD-95 (H372A mutant) 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 / juxtaparanode region of axon / frizzled binding / neuron projection terminus / acetylcholine receptor binding / 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 / kinesin binding / regulation of neuronal synaptic plasticity / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / D1 dopamine receptor binding / positive regulation of synaptic transmission / 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 / spliceosomal complex / neuromuscular junction / 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 / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / neuronal cell body / dendrite / synapse / 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: 1.851 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)13,7872
Polymers13,7872
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.445, 89.445, 89.445
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-557-

HOH

21B-107-

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: 1116.266 Da / Num. of mol.: 1 / Fragment: PDZ3-binding domain (UNP residues 93-101) / Mutation: T99F / 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.: 124 / 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: 2.15 Å3/Da / Density % sol: 43 %
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 1.05 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 1.05 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (7 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 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.851→40.001 Å / Num. obs: 10760 / % possible obs: 98.22 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 35.543
Reflection shellResolution: 1.8514→1.9357 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1 / % possible all: 88

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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: 1.851→40.001 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1078 10.02 %random selection
Rwork0.1841 ---
obs0.1865 10760 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.851→40.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 0 124 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121060
X-RAY DIFFRACTIONf_angle_d1.4621444
X-RAY DIFFRACTIONf_dihedral_angle_d23.328405
X-RAY DIFFRACTIONf_chiral_restr0.733155
X-RAY DIFFRACTIONf_plane_restr0.021203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8514-1.93570.31431170.291054X-RAY DIFFRACTION88
1.9357-2.03770.23131330.20561195X-RAY DIFFRACTION100
2.0377-2.16540.21181320.19231190X-RAY DIFFRACTION100
2.1654-2.33260.25961340.19741204X-RAY DIFFRACTION100
2.3326-2.56730.18031370.18541223X-RAY DIFFRACTION100
2.5673-2.93870.21031360.17921222X-RAY DIFFRACTION100
2.9387-3.7020.19241390.1711258X-RAY DIFFRACTION100
3.702-40.01030.18981500.16971336X-RAY DIFFRACTION99
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)
10.7728-1.00620.47281.77640.6523.72260.1968-0.49190.20450.43230.0165-0.7874-0.15891.2197-0.25160.42820.0052-0.11470.550.03970.706860.816766.779446.7452
22.41180.2167-0.33052.59470.02953.388-0.0578-0.38340.14550.11020.0617-0.2706-0.01070.1172-0.06710.2178-0.0091-0.01340.18780.00440.187142.426964.806841.6167
32.4402-0.5185-0.52132.1475-0.55634.5146-0.05680.1692-0.0944-0.11440.07170.1090.178-0.2697-0.06480.1336-0.01310.00440.18110.00690.133739.456359.991926.8521
42.42430.3943-0.91762.0785-0.22472.90250.0698-0.16010.07920.0331-0.0233-0.0142-0.1376-0.1633-0.04860.16460.0028-0.00780.16670.00650.138636.667361.873934.1932
53.70330.3201-0.4847.8351-2.79093.9631-0.11710.3621-0.1049-0.3560.55050.38070.3398-0.6138-0.0080.1606-0.0281-0.0260.3080.02810.137230.381657.90524.2635
62.054-0.8994-0.29871.67520.72912.9888-0.0783-0.0249-0.05380.04720.17370.03070.0667-0.0956-0.04470.1269-0.02240.00860.15350.02530.157839.905857.017233.896
73.9328-0.2578-0.14625.3151-0.223.90040.20430.30560.20710.0461-0.1691-0.5410.15430.861-0.16940.24240.0927-0.07580.2923-0.0190.251853.45352.53238.4444
84.2916-3.35090.40283.3526-2.25085.2695-0.10780.0702-0.488-0.18560.14550.3920.95820.0416-0.06850.33460.0120.02840.17670.00240.254838.496452.586122.4799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 299:303)
2X-RAY DIFFRACTION2(chain A and resid 304:317)
3X-RAY DIFFRACTION3(chain A and resid 318:346)
4X-RAY DIFFRACTION4(chain A and resid 347:369)
5X-RAY DIFFRACTION5(chain A and resid 370:380)
6X-RAY DIFFRACTION6(chain A and resid 381:403)
7X-RAY DIFFRACTION7(chain A and resid 404:415)
8X-RAY DIFFRACTION8(chain B and resid 3:9)

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