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- PDB-1ddv: CRYSTAL STRUCTURE OF THE HOMER EVH1 DOMAIN WITH BOUND MGLUR PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1ddv
TitleCRYSTAL STRUCTURE OF THE HOMER EVH1 DOMAIN WITH BOUND MGLUR PEPTIDE
Components
  • GLGF-DOMAIN PROTEIN HOMER
  • METABOTROPIC GLUTAMATE RECEPTOR MGLUR5
KeywordsSIGNALING PROTEIN / PROTEIN-LIGAND COMPLEX / POLYPROLINE RECOGNITION / BETA TURN
Function / homology
Function and homology information


: / PLC activating G protein-coupled glutamate receptor activity / : / negative regulation of locomotion / G protein-coupled glutamate receptor binding / Class C/3 (Metabotropic glutamate/pheromone receptors) / structural constituent of postsynapse / : / A2A adenosine receptor binding / : ...: / PLC activating G protein-coupled glutamate receptor activity / : / negative regulation of locomotion / G protein-coupled glutamate receptor binding / Class C/3 (Metabotropic glutamate/pheromone receptors) / structural constituent of postsynapse / : / A2A adenosine receptor binding / : / regulation of translational elongation / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / regulation of dendritic spine maintenance / regulation of store-operated calcium entry / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / Neurexins and neuroligins / positive regulation of long-term neuronal synaptic plasticity / : / desensitization of G protein-coupled receptor signaling pathway / regulation of calcium ion import / G protein-coupled glutamate receptor signaling pathway / protein localization to synapse / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / astrocyte projection / neuron spine / costamere / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of calcium ion transport / phosphatidylinositol-mediated signaling / glutamate receptor activity / G alpha (q) signalling events / type 5 metabotropic glutamate receptor binding / postsynaptic cytosol / postsynaptic modulation of chemical synaptic transmission / plasma membrane => GO:0005886 / behavioral response to cocaine / : / skeletal muscle contraction / positive regulation of protein tyrosine kinase activity / skeletal muscle fiber development / regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / response to cocaine / dendritic shaft / locomotory behavior / response to nicotine / learning / PDZ domain binding / G protein-coupled receptor activity / postsynaptic density membrane / protein tetramerization / synapse organization / regulation of long-term neuronal synaptic plasticity / regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / cognition / Z disc / response to calcium ion / circadian rhythm / cellular response to amyloid-beta / apical part of cell / chemical synaptic transmission / postsynapse / scaffold protein binding / postsynaptic membrane / transmembrane transporter binding / dendritic spine / postsynaptic density / learning or memory / molecular adaptor activity / calmodulin binding / neuron projection / axon / protein phosphorylation / signaling receptor binding / neuronal cell body / dendrite / glutamatergic synapse / protein-containing complex binding / regulation of DNA-templated transcription / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Homer, EVH1 domain / Homer family / GPCR, family 3, metabotropic glutamate receptor 5 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 ...Homer, EVH1 domain / Homer family / GPCR, family 3, metabotropic glutamate receptor 5 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Metabotropic glutamate receptor 5 / Homer protein homolog 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBeneken, J. / Tu, J.C. / Xiao, B. / Worley, P.F. / Leahy, D.J.
Citation
Journal: Neuron / Year: 2000
Title: Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition.
Authors: Beneken, J. / Tu, J.C. / Xiao, B. / Nuriya, M. / Yuan, J.P. / Worley, P.F. / Leahy, D.J.
#1: Journal: Neuron / Year: 1998
Title: Homer binds a novel proline-rich motif and links group 1 metabotropic glutamate receptors with IP3 receptors
Authors: Tu, J.C. / Xiao, B. / Yuan, J.P. / Lanahan, A.A. / Worley, P.F. / Leoffert, K. / Li, M. / Linden, D.J.
History
DepositionNov 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: GLGF-DOMAIN PROTEIN HOMER
B: METABOTROPIC GLUTAMATE RECEPTOR MGLUR5


Theoretical massNumber of molelcules
Total (without water)13,3332
Polymers13,3332
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-6 kcal/mol
Surface area6640 Å2
MethodPISA
2
A: GLGF-DOMAIN PROTEIN HOMER
B: METABOTROPIC GLUTAMATE RECEPTOR MGLUR5

A: GLGF-DOMAIN PROTEIN HOMER
B: METABOTROPIC GLUTAMATE RECEPTOR MGLUR5


Theoretical massNumber of molelcules
Total (without water)26,6664
Polymers26,6664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2550 Å2
ΔGint-18 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.7, 48.6, 35.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GLGF-DOMAIN PROTEIN HOMER


Mass: 12688.221 Da / Num. of mol.: 1 / Fragment: HOMER EVH1 RESIDUES 1-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z214
#2: Protein/peptide METABOTROPIC GLUTAMATE RECEPTOR MGLUR5


Mass: 644.715 Da / Num. of mol.: 1 / Fragment: MGLUR DERIVED PEPTIDE TPPSPF / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN NORWAY RAT (RATTUS NORVEGICUS)
References: UniProt: P31424
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.82 Å3/Da / Density % sol: 32.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, SODIUM ACETATE, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 mg/mlpeptide1drop
330 %PEG33501reservoir
4100 mMsodium acetate1reservoir
5100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 7996 / Num. obs: 7996 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 28
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.377 / % possible all: 87
Reflection
*PLUS
Reflection shell
*PLUS
Mean I/σ(I) obs: 5.1

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.278 818 RANDOM
Rwork0.242 --
obs0.242 7732 -
all-8105 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 76 966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
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_deg1.376
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.241 / Rfactor Rfree: 0.289 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0187
X-RAY DIFFRACTIONc_angle_deg1.924

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