[English] 日本語
Yorodumi
- PDB-1ddv: CRYSTAL STRUCTURE OF THE HOMER EVH1 DOMAIN WITH BOUND MGLUR PEPTIDE -

+
Open data


ID or keywords:

Loading...

-
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 / G protein-coupled glutamate receptor binding / structural constituent of postsynapse / Class C/3 (Metabotropic glutamate/pheromone receptors) / regulation of dendritic spine maintenance / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / regulation of store-operated calcium entry ...PLC activating G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor binding / structural constituent of postsynapse / Class C/3 (Metabotropic glutamate/pheromone receptors) / regulation of dendritic spine maintenance / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / regulation of store-operated calcium entry / Neurexins and neuroligins / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / regulation of calcium ion import / neuron spine / protein localization to synapse / G protein-coupled glutamate receptor signaling pathway / costamere / astrocyte projection / positive regulation of calcium ion transport / type 5 metabotropic glutamate receptor binding / glutamate receptor activity / G alpha (q) signalling events / phosphatidylinositol-mediated signaling / behavioral response to cocaine / protein tyrosine kinase activator activity / postsynaptic cytosol / excitatory synapse / skeletal muscle contraction / regulation of synaptic transmission, glutamatergic / skeletal muscle fiber development / positive regulation of calcium-mediated signaling / dendritic shaft / protein tyrosine kinase binding / learning / PDZ domain binding / locomotory behavior / protein tetramerization / response to nicotine / response to cocaine / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / synapse organization / postsynaptic density membrane / G protein-coupled receptor activity / Schaffer collateral - CA1 synapse / Z disc / cognition / response to calcium ion / circadian rhythm / cellular response to amyloid-beta / apical part of cell / scaffold protein binding / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / molecular adaptor activity / dendritic spine / transmembrane transporter binding / postsynaptic membrane / learning or memory / postsynapse / positive regulation of MAPK cascade / calmodulin binding / neuron projection / postsynaptic density / protein phosphorylation / axon / signaling receptor binding / neuronal cell body / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / identical protein binding / membrane / 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 / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more