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- PDB-1i2h: CRYSTAL STRUCTURE ANALYSIS OF PSD-ZIP45(HOMER1C/VESL-1L)CONSERVED... -

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Basic information

Entry
Database: PDB / ID: 1i2h
TitleCRYSTAL STRUCTURE ANALYSIS OF PSD-ZIP45(HOMER1C/VESL-1L)CONSERVED HOMER 1 DOMAIN
ComponentsPSD-ZIP45(HOMER-1C/VESL-1L)
KeywordsSIGNALING PROTEIN / ENABLED VASP HOMOLOGY 1 domain
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 / protein localization to synapse / G protein-coupled glutamate receptor signaling pathway / 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 / protein localization to synapse / G protein-coupled glutamate receptor signaling pathway / 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 / response to cocaine / dendritic shaft / protein tetramerization / response to nicotine / Z disc / response to calcium ion / circadian rhythm / apical part of cell / scaffold protein binding / postsynapse / transmembrane transporter binding / dendritic spine / molecular adaptor activity / postsynaptic density / neuron projection / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIrie, K. / Nakatsu, T. / Mitsuoka, K. / Fujiyoshi, Y. / Kato, H.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of the Homer 1 Family Conserved Region Reveals the Interaction Between the EVH1 Domain and Own Proline-rich Motif
Authors: Irie, K. / Nakatsu, T. / Mitsuoka, K. / Miyazawa, A. / Sobue, K. / Hiroaki, Y. / Doi, T. / Fujiyoshi, Y. / Kato, H.
#1: Journal: FEBS Lett. / Year: 1998
Title: Isolation of PSD-Zip45, a Novel Homer/vesl Family Protein Containing Leucine Zipper Motifs, from Rat Brain.
Authors: Sun, J. / Tadokoro, S. / Imanaka, T. / Murakami, S.D. / Nakamura, M. / Kashiwada, K. / Ko, J. / Nishida, W. / Sobue, K.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Involvement of unique leucine-zipper motif of PSD-Zip45 (Homer 1c/vesl-1L) in group 1 metabotropic glutamate receptor clustering.
Authors: Tadokoro, S. / Tachibana, T. / Imanaka, T. / Nishida, W. / Sobue, K.
History
DepositionFeb 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). IT IS UNCLEAR WHETHER THE BIOLOGICAL UNIT IS A MONOMER OR DIMER.
Remark 999SEQUENCE FIVE RESIDUES (GSPEF) INSERTED AT N-TERMINUS COME FROM PGEX-4T-1. The EcoRI and Xho I site ...SEQUENCE FIVE RESIDUES (GSPEF) INSERTED AT N-TERMINUS COME FROM PGEX-4T-1. The EcoRI and Xho I site of pGEX-4T-1 is used for cloning. The GST-fusion linker, GSPEF, is located after the thrombin cleavage site and before the EcoRI site. These fusion linker residues are numbered 996-1000.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSD-ZIP45(HOMER-1C/VESL-1L)


Theoretical massNumber of molelcules
Total (without water)18,8241
Polymers18,8241
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.262, 71.153, 39.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-38-

HOH

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Components

#1: Protein PSD-ZIP45(HOMER-1C/VESL-1L)


Mass: 18823.729 Da / Num. of mol.: 1 / Fragment: N-TERMINAL CONSERVED HOMER 1 REGION (CH1 DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PSD-ZIP45 / Organ: BRAIN / Plasmid: PGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z214
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
123 mg/mlprotein1drop
21.1 Msodium citrate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 1, 2000
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.8→200 Å / Num. all: 15030 / Num. obs: 14936 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.26 % / Rmerge(I) obs: 0.268 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 50784 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.268

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDW

1ddw


Resolution: 1.8→19.09 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 753 -RANDOM
Rwork0.195 ---
all0.224 15009 --
obs0.223 14936 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→19.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 114 1170
LS refinement shellResolution: 1.8→1.885 Å /
RfactorNum. reflection
Rfree0.27 94
Rwork0.24 -
obs-1758
Refinement
*PLUS
Lowest resolution: 19.09 Å / % reflection Rfree: 5 % / Rfactor all: 0.224 / Rfactor obs: 0.195 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0196
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg2.1684
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / Rfactor Rwork: 0.24

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