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- PDB-1n7f: Crystal structure of the sixth PDZ domain of GRIP1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1n7f
TitleCrystal structure of the sixth PDZ domain of GRIP1 in complex with liprin C-terminal peptide
Components
  • 8-mer peptide from interacting protein (liprin)
  • AMPA receptor interacting protein GRIP
KeywordsPROTEIN BINDING / PDZ / grip / liprin
Function / homology
Function and homology information


regulation of synaptic scaling / spine apparatus / exocyst / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / positive regulation of neuron projection arborization / Serotonin Neurotransmitter Release Cycle / neurotransmitter receptor transport, endosome to postsynaptic membrane / dendrite arborization / vesicle-mediated transport in synapse ...regulation of synaptic scaling / spine apparatus / exocyst / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / positive regulation of neuron projection arborization / Serotonin Neurotransmitter Release Cycle / neurotransmitter receptor transport, endosome to postsynaptic membrane / dendrite arborization / vesicle-mediated transport in synapse / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / cortical microtubule organization / cellular response to phorbol 13-acetate 12-myristate / positive regulation of dendrite morphogenesis / proximal dendrite / presynaptic active zone / negative regulation of stress fiber assembly / spine synapse / dendritic spine neck / dendritic spine head / Trafficking of GluR2-containing AMPA receptors / negative regulation of protein localization to plasma membrane / synaptic cleft / regulation of postsynaptic membrane neurotransmitter receptor levels / cellular response to brain-derived neurotrophic factor stimulus / ionotropic glutamate receptor binding / synaptic membrane / cell-matrix adhesion / dendritic shaft / positive regulation of protein localization to plasma membrane / PDZ domain binding / synapse organization / recycling endosome / cerebral cortex development / GABA-ergic synapse / Schaffer collateral - CA1 synapse / terminal bouton / intracellular protein localization / nervous system development / presynapse / presynaptic membrane / GTPase binding / cell cortex / perikaryon / dendritic spine / microtubule / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / membrane raft / signaling receptor binding / axon / focal adhesion / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / protein-containing complex / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Glutamate receptor-interacting protein 1/2 / Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / PDZ domain 6 / PDZ domain / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / PDZ domain ...Glutamate receptor-interacting protein 1/2 / Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / PDZ domain 6 / PDZ domain / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
: / Glutamate receptor-interacting protein 1 / Liprin-alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIm, Y.J. / Park, S.H. / Rho, S.H. / Lee, J.H. / Kang, G.B. / Sheng, M. / Kim, E. / Eom, S.H.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization
Authors: Im, Y.J. / Park, S.H. / Rho, S.H. / Lee, J.H. / Kang, G.B. / Sheng, M. / Kim, E. / Eom, S.H.
History
DepositionNov 14, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMPA receptor interacting protein GRIP
B: AMPA receptor interacting protein GRIP
C: 8-mer peptide from interacting protein (liprin)
D: 8-mer peptide from interacting protein (liprin)


Theoretical massNumber of molelcules
Total (without water)22,0874
Polymers22,0874
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-20 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.790, 117.790, 101.974
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein AMPA receptor interacting protein GRIP / glutamate receptor interacting protein 1


Mass: 10142.639 Da / Num. of mol.: 2 / Fragment: sixth PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: grip1 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P97879
#2: Protein/peptide 8-mer peptide from interacting protein (liprin)


Mass: 901.020 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The sequence of this chemically synthetized octa peptide occurs in the C-termiuns of human liprin alpha protein
References: GenBank: 21707845, UniProt: Q13136*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.96 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG400, MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Park, S.H., (2002) Acta Cryst., D58, 1063.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 192446 / Num. obs: 191677 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.58 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.89 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.566 / % possible all: 97.3
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.26 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure solved by Br-MAD phasing of peptide free crystal
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1822 7.3 %RANDOM
Rwork0.2 ---
all0.2024 ---
obs0.2 24896 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4386 Å2 / ksol: 0.35575 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å2-0.88 Å20 Å2
2---2 Å20 Å2
3---5.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 236 1644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.232 3930 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMCNS_PROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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