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- PDB-5hf1: The third PDZ domain from the synaptic protein PSD-95 (G330T muta... -

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Basic information

Entry
Database: PDB / ID: 5hf1
TitleThe third PDZ domain from the synaptic protein PSD-95 (G330T 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


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 / structural constituent of postsynaptic density / protein localization to microtubule ...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 / structural constituent of postsynaptic density / protein localization to microtubule / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / LGI-ADAM interactions / proximal dendrite / neuron spine / Trafficking of AMPA receptors / protein localization to synapse / regulation of postsynaptic density assembly / AMPA glutamate receptor clustering / cellular response to potassium ion / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of dendrite morphogenesis / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / dendritic spine organization / regulation of NMDA receptor activity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / NMDA selective glutamate receptor signaling pathway / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / kinesin binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / postsynaptic density, intracellular component / glutamate receptor binding / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / cytoplasmic microtubule organization / dendrite cytoplasm / RNA splicing / dendritic shaft / cell periphery / PDZ domain binding / spliceosomal complex / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / neuromuscular junction / cerebral cortex development / cell-cell adhesion / kinase binding / mRNA processing / cell junction / synaptic vesicle / cell-cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / microtubule binding / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm
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: 1.747 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)13,8982
Polymers13,8982
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.724, 89.724, 89.724
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
11B-101-

HOH

21B-102-

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: 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.: 102 / 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: 43.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
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 6.8. 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 6.8. 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791833 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791833 Å / Relative weight: 1
ReflectionResolution: 1.747→40.126 Å / Num. obs: 13010 / % possible obs: 99.48 % / Redundancy: 27.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 67.804
Reflection shellResolution: 1.7469→1.8169 Å / Redundancy: 26.3 % / Mean I/σ(I) obs: 1.844

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BE9

1be9


Resolution: 1.747→40.126 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1301 10 %random selection
Rwork0.1993 ---
obs0.2012 13010 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.747→40.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 102 1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061106
X-RAY DIFFRACTIONf_angle_d0.9371508
X-RAY DIFFRACTIONf_dihedral_angle_d24.464422
X-RAY DIFFRACTIONf_chiral_restr0.05164
X-RAY DIFFRACTIONf_plane_restr0.003209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7469-1.81690.30341350.28831224X-RAY DIFFRACTION96
1.8169-1.89950.26871420.24961264X-RAY DIFFRACTION100
1.8995-1.99970.22891420.23411280X-RAY DIFFRACTION100
1.9997-2.1250.25231410.20071274X-RAY DIFFRACTION100
2.125-2.2890.22641450.20441301X-RAY DIFFRACTION100
2.289-2.51930.20891430.18691286X-RAY DIFFRACTION100
2.5193-2.88380.19811460.19011315X-RAY DIFFRACTION100
2.8838-3.63290.19941490.18711336X-RAY DIFFRACTION100
3.6329-40.13640.20881580.18691429X-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)
13.5332-0.2989-0.9392.9435-0.11722.0108-0.128-0.49670.5162-0.0076-0.0161-0.4498-0.23320.37040.17450.2221-0.0014-0.03430.24230.04010.210446.155965.633742.7345
23.7941-0.11640.17291.8769-0.23972.9213-0.0270.3514-0.0553-0.47330.07330.08120.1056-0.1669-0.01610.22810.0123-0.01440.12440.00960.111840.282662.682926.6578
34.0126-1.24430.7442.8302-1.16644.1726-0.00740.1674-0.0107-0.40990.0780.33910.103-0.4435-0.07270.20510.0107-0.05380.16110.04860.168134.320661.427731.7873
46.3531-1.84040.81817.10240.55936.5973-0.37750.057-0.22380.28240.3223-0.04140.41290.40320.00920.22010.07330.05330.11030.04150.156549.653350.745436.5733
59.3796-5.1042.27313.2076-2.18663.73950.30460.0012-0.5359-0.2111-0.33880.31750.7747-0.12580.08990.66420.0324-0.08480.2278-0.02310.445938.984354.00822.3213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 299 through 317 )
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 350 )
3X-RAY DIFFRACTION3chain 'A' and (resid 351 through 392 )
4X-RAY DIFFRACTION4chain 'A' and (resid 393 through 415 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 9 )

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