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- PDB-1ddw: HOMER EVH1 DOMAIN UNLIGANDED -

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Basic information

Entry
Database: PDB / ID: 1ddw
TitleHOMER EVH1 DOMAIN UNLIGANDED
ComponentsGLGF-DOMAIN PROTEIN HOMER
KeywordsSIGNALING PROTEIN / PLECKSTRIN HOMOLOGY DOMAIN FOLD
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / structural constituent of postsynapse / regulation of dendritic spine maintenance / regulation of store-operated calcium entry / Neurexins and neuroligins / regulation of calcium ion import / G protein-coupled glutamate receptor signaling pathway / protein localization to synapse / neuron spine / costamere ...G protein-coupled glutamate receptor binding / structural constituent of postsynapse / regulation of dendritic spine maintenance / regulation of store-operated calcium entry / Neurexins and neuroligins / regulation of calcium ion import / G protein-coupled glutamate receptor signaling pathway / protein localization to synapse / neuron spine / costamere / positive regulation of calcium ion transport / type 5 metabotropic glutamate receptor binding / postsynaptic cytosol / behavioral response to cocaine / skeletal muscle contraction / skeletal muscle fiber development / regulation of synaptic transmission, glutamatergic / dendritic shaft / response to nicotine / response to cocaine / protein tetramerization / Z disc / response to calcium ion / circadian rhythm / apical part of cell / scaffold protein binding / postsynapse / transmembrane transporter binding / dendritic spine / postsynaptic density / molecular adaptor activity / neuron projection / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Homer, EVH1 domain / Homer family / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Homer protein homolog 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLGF-DOMAIN PROTEIN HOMER


Theoretical massNumber of molelcules
Total (without water)13,8271
Polymers13,8271
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.94, 49.94, 80.91
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GLGF-DOMAIN PROTEIN HOMER


Mass: 13827.220 Da / Num. of mol.: 1 / Fragment: HOMER EVH1 DOMAIN RESIDUES 1-120 / Mutation: NONE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PGEX / Production host: Bacteria (eubacteria) / References: UniProt: Q9Z214
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, Magnesium sulfate, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
230 %PEG33501reservoir
387 mM1reservoirMgSO4
450 mMHEPES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
3931
4931
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X4A10.9879
SYNCHROTRONNSLS X4A20.9793
SYNCHROTRONNSLS X4A30.979
SYNCHROTRONNSLS X4A40.9611
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEOct 30, 1998
RIGAKU RAXIS IV2IMAGE PLATEOct 30, 1998
RIGAKU RAXIS IV3IMAGE PLATEOct 30, 1998
RIGAKU RAXIS IV4IMAGE PLATEOct 30, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98791
20.97931
30.9791
40.96111
ReflectionResolution: 1.7→30 Å / Num. all: 13342 / Num. obs: 12725 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 21
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 2.34 % / Rmerge(I) obs: 0.286 / % possible all: 77
Reflection
*PLUS
Num. obs: 24051 / % possible obs: 96.8 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 1.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflectionSelection details
Rfree0.285 1313 RANDOM
Rwork0.245 --
obs0.245 12725 -
all-13357 -
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 0 88 984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0126
X-RAY DIFFRACTIONc_angle_deg1.745
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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