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- PDB-5hey: The third PDZ domain from the synaptic protein PSD-95 (G330T muta... -

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Basic information

Entry
Database: PDB / ID: 5hey
TitleThe third PDZ domain from the synaptic protein PSD-95 (G330T 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


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 / acetylcholine receptor binding / neuron projection terminus / 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 / kinesin binding / social behavior / 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 / regulation of long-term neuronal synaptic plasticity / cell-cell adhesion / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)13,8522
Polymers13,8522
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-4 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.230, 90.230, 90.230
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-642-

HOH

21B-101-

HOH

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Components

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


Mass: 12782.120 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402) / Mutation: G330T
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 / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q792Q4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
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 1.2 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.5→28.533 Å / Num. obs: 20266 / % possible obs: 97.95 % / Redundancy: 21.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 30.057
Reflection shellResolution: 1.5003→1.5378 Å / Redundancy: 14.7 % / % possible all: 78

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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: 1.5→28.533 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 2024 9.99 %random selection
Rwork0.1724 ---
obs0.1754 20266 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→28.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 0 147 1112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111151
X-RAY DIFFRACTIONf_angle_d1.8431580
X-RAY DIFFRACTIONf_dihedral_angle_d19.935443
X-RAY DIFFRACTIONf_chiral_restr0.057172
X-RAY DIFFRACTIONf_plane_restr0.017224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5003-1.53780.28541120.27041010X-RAY DIFFRACTION78
1.5378-1.57940.25381370.25461230X-RAY DIFFRACTION95
1.5794-1.62590.27871390.23221275X-RAY DIFFRACTION99
1.6259-1.67830.24571440.21791292X-RAY DIFFRACTION100
1.6783-1.73830.25461440.2181303X-RAY DIFFRACTION100
1.7383-1.80790.24521460.19681306X-RAY DIFFRACTION100
1.8079-1.89020.22341450.18051313X-RAY DIFFRACTION100
1.8902-1.98980.19661460.17321316X-RAY DIFFRACTION100
1.9898-2.11440.22111460.16381317X-RAY DIFFRACTION100
2.1144-2.27760.19311490.14891336X-RAY DIFFRACTION100
2.2776-2.50670.18761490.15071340X-RAY DIFFRACTION100
2.5067-2.86910.19141490.15391337X-RAY DIFFRACTION100
2.8691-3.61360.17081540.15511387X-RAY DIFFRACTION100
3.6136-28.53840.1891640.17081480X-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)
10.02470.01750.03110.038-0.03030.0859-0.2583-0.2419-0.59420.2802-0.14340.6248-0.0235-0.3956-00.3571-0.0245-0.01040.41080.1050.533550.427670.173439.3116
20.02310.0226-0.03760.05950.0030.03860.0535-0.2907-0.28560.09520.59310.36850.29150.4888-00.2945-0.015-0.01020.5568-0.0760.572654.68863.432744.9411
30.4742-0.0321-0.40790.42320.17520.4234-0.3192-0.1169-0.07350.35130.1962-0.4993-0.19190.4063-0.06780.2115-0.0485-0.0930.20440.02210.255149.817261.583546.3906
40.080.1284-0.11960.1798-0.17290.1286-0.0567-0.15160.16430.13960.0131-0.1817-0.1775-0.006200.16560.0088-0.00860.14530.00580.098938.929163.190443.765
50.2872-0.1709-0.16520.05330.08880.0892-0.1350.2710.22120.141-0.1265-0.058-0.9145-0.0771-0.11050.2119-0.0017-0.00410.1760.0680.12336.420473.058527.4521
60.3187-0.24440.21660.56590.10680.36530.05670.32460.03180.0739-0.1961-0.13120.1428-0.1093-0.03080.1198-0.02260.01640.15380.0010.103240.08359.73826.29
70.18370.43590.04481.01060.16250.0596-0.1344-0.1337-0.3258-0.5032-0.28470.14980.2176-0.1269-0.50530.1341-0.2555-0.0661-0.0768-0.01840.36133.17447.669631.3353
80.1413-0.10930.07690.2243-0.05930.41790.07220.00640.04290.0554-0.1308-0.1437-0.04960.0603-0.0180.0969-0.01710.00490.12680.01880.109644.355963.622428.5422
90.29960.1345-0.0040.1525-0.21030.50010.1195-0.05160.19540.1172-0.1733-0.1619-0.24120.0989-0.00010.1552-0.0204-0.00720.11860.02640.169143.811365.953234.9639
100.23510.1025-0.23180.31570.28690.3378-0.00260.0497-0.0613-0.06220.02190.3160.1251-0.24350.02090.0999-0.0127-0.01160.17120.02380.138929.870159.154533.6674
110.0571-0.06880.0780.3263-0.2440.1839-0.12580.5143-0.0907-0.39770.4570.5329-0.028-0.41050.10760.1284-0.0391-0.04280.27020.0350.142230.642658.809123.6879
120.90771.2960.03722.07570.17120.0683-0.07090.17620.03210.21230.64220.2695-0.3775-0.48740.58870.30920.1240.03190.29850.16190.199629.983172.319524.9525
130.5517-0.2529-0.74350.31380.2141.0647-0.0452-0.0035-0.12560.07320.07050.0840.0481-0.12990.04130.0988-0.0019-0.00930.10570.01260.104439.377659.284337.2302
140.1482-0.07150.03240.14580.07970.3343-0.0917-0.17360.17330.06190.13330.30950.0481-0.50670.01340.2365-0.02220.03270.2111-0.01890.127446.099547.509932.7856
150.58010.542-0.30450.6393-0.49550.35870.02080.08220.15160.0155-0.0552-0.3410.02510.1495-0.00010.1564-0.0017-0.01250.128-0.00050.124153.80751.870738.2074
160.22340.0917-0.1640.6061-0.19090.366-0.0920.1841-0.3858-0.95120.05810.15890.51190.0615-0.00290.2777-0.0028-0.02940.2426-0.04210.278739.285151.845123.5241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 297:300)
2X-RAY DIFFRACTION2(chain A and resid 301:304)
3X-RAY DIFFRACTION3(chain A and resid 305:308)
4X-RAY DIFFRACTION4(chain A and resid 309:313)
5X-RAY DIFFRACTION5(chain A and resid 314:321)
6X-RAY DIFFRACTION6(chain A and resid 322:329)
7X-RAY DIFFRACTION7(chain A and resid 330:335)
8X-RAY DIFFRACTION8(chain A and resid 336:348)
9X-RAY DIFFRACTION9(chain A and resid 349:358)
10X-RAY DIFFRACTION10(chain A and resid 359:371)
11X-RAY DIFFRACTION11(chain A and resid 372:380)
12X-RAY DIFFRACTION12(chain A and resid 381:384)
13X-RAY DIFFRACTION13(chain A and resid 385:397)
14X-RAY DIFFRACTION14(chain A and resid 398:402)
15X-RAY DIFFRACTION15(chain A and resid 403:415)
16X-RAY DIFFRACTION16(chain B)

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