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- PDB-2p8v: Crystal structure of human Homer3 EVH1 domain -

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Basic information

Entry
Database: PDB / ID: 2p8v
TitleCrystal structure of human Homer3 EVH1 domain
ComponentsHomer protein homolog 3
KeywordsSIGNALING PROTEIN / Homer3 / EVH1 domain
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / regulation of store-operated calcium entry / basal part of cell / G protein-coupled glutamate receptor signaling pathway / Neurexins and neuroligins / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / protein targeting / postsynaptic density / protein domain specific binding ...G protein-coupled glutamate receptor binding / regulation of store-operated calcium entry / basal part of cell / G protein-coupled glutamate receptor signaling pathway / Neurexins and neuroligins / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / protein targeting / postsynaptic density / protein domain specific binding / glutamatergic synapse / dendrite / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBouyain, S. / Tu, J. / Huang, G.N. / Worley, P.F. / Leahy, D.
CitationJournal: Science / Year: 2008
Title: NFAT binding and regulation of T cell activation by the cytoplasmic scaffolding Homer proteins.
Authors: Huang, G.N. / Huso, D.L. / Bouyain, S. / Tu, J. / McCorkell, K.A. / May, M.J. / Zhu, Y. / Lutz, M. / Collins, S. / Dehoff, M. / Kang, S. / Whartenby, K. / Powell, J. / Leahy, D. / Worley, P.F.
History
DepositionMar 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homer protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2712
Polymers13,1751
Non-polymers961
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.470, 49.470, 80.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Homer protein homolog 3 / Homer-3


Mass: 13174.810 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOMER3 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9NSC5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M HEPES pH 7.0-7.4, 30% PEG3350, 105 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 10075 / % possible obs: 98.8 % / Rmerge(I) obs: 0.078 / Χ2: 1.01 / Net I/σ(I): 20.3
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.493 / Num. unique all: 930 / Χ2: 1.082 / % possible all: 94

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Phasing

Phasing MRRfactor: 0.42 / Cor.coef. Fo:Fc: 0.601
Highest resolutionLowest resolution
Rotation3 Å29.35 Å
Translation3 Å29.35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDW

1ddw


Resolution: 1.85→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.264 1018 10 %
Rwork0.222 --
obs-9808 96 %
Solvent computationBsol: 38.076 Å2
Displacement parametersBiso mean: 26.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.703 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 5 74 1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.311
X-RAY DIFFRACTIONc_mcbond_it2.6141.5
X-RAY DIFFRACTIONc_scbond_it4.032
X-RAY DIFFRACTIONc_mcangle_it3.62
X-RAY DIFFRACTIONc_scangle_it5.5792.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5sulf.paramsulf.top

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