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- PDB-9qux: Solution structure of the Homer1 EVH1 domain -

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Basic information

Entry
Database: PDB / ID: 9qux
TitleSolution structure of the Homer1 EVH1 domain
ComponentsHomer protein homolog 1
KeywordsPEPTIDE BINDING PROTEIN / Postsynapse / Enabled/VASP homology 1 domain
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / Neurexins and neuroligins / regulation of dendritic spine maintenance / regulation of store-operated calcium entry / regulation of calcium ion import / neuron spine / costamere / G protein-coupled glutamate receptor signaling pathway / positive regulation of calcium ion transport / skeletal muscle contraction ...G protein-coupled glutamate receptor binding / Neurexins and neuroligins / regulation of dendritic spine maintenance / regulation of store-operated calcium entry / regulation of calcium ion import / neuron spine / costamere / G protein-coupled glutamate receptor signaling pathway / positive regulation of calcium ion transport / skeletal muscle contraction / postsynaptic cytosol / regulation of synaptic transmission, glutamatergic / skeletal muscle fiber development / behavioral response to cocaine / protein tetramerization / response to calcium ion / Z disc / apical part of cell / dendritic spine / transmembrane transporter binding / postsynapse / neuron projection / postsynaptic density / axon / glutamatergic synapse / membrane / plasma membrane / cytoplasm
Similarity search - Function
Homer, EVH1 domain / Homer family / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / PH-like domain superfamily
Similarity search - Domain/homology
Homer protein homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsCzajlik, A. / Maruzs, B. / Fanni, F. / Batta, G. / Gaspari, Z. / Peterfia, B.F.
Funding support Hungary, 1items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)OTKA 137947 Hungary
CitationJournal: Proteins / Year: 2025
Title: Structural Modeling and Dynamics of the Full-Length Homer1 Multimer.
Authors: Kalman, Z.E. / Czajlik, A. / Maruzs, B. / Farkas, F. / Pap, I. / Homonnay, C. / Klumpler, T. / Batta, G. / Gaspari, Z. / Peterfia, B.
History
DepositionApr 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Homer protein homolog 1


Theoretical massNumber of molelcules
Total (without water)13,7571
Polymers13,7571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Homer protein homolog 1 / Homer-1 / VASP/Ena-related gene up-regulated during seizure and LTP 1 / Vesl-1


Mass: 13757.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Homer1, Vesl1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z2Y3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-15N TOCSY
141isotropic13D HNCA
151isotropic13D HN(CA)CB
1151isotropic13D HN(CO)CA
1141isotropic13D HN(COCA)CB
1131isotropic13D HNCO
1121isotropic13D HCACO
1111isotropic12D 1H-13C HSQC
1101isotropic12D 1H-15N HSQC
191isotropic13D HCAN
181isotropic12D (HB)CB(CGCD)HD
171isotropic13D H(CCO)NH
161isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 180 uM [U-13C; U-15N] Homer1 EVH1, 50 mM Sodium phosphate buffer, 20 mM sodium chloride, 0.02 % NaN3, 95% H2O/5% D2O
Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
180 uMHomer1 EVH1[U-13C; U-15N]1
50 mMSodium phosphate buffernatural abundance1
20 mMsodium chloridenatural abundance1
0.02 %NaN3natural abundance1
Sample conditionsIonic strength: 215 mM / Label: conditions_1 / pH: 7.36 / PH err: 0.02 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5.2CCPNpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 3
Details: From the 20 CYANA-calculated conformers, each was subjected to a gentle simulated annealing protocol with an upper temperature of 150 C to calculate 20 conformers from which the one with the ...Details: From the 20 CYANA-calculated conformers, each was subjected to a gentle simulated annealing protocol with an upper temperature of 150 C to calculate 20 conformers from which the one with the lowest energy was retained.
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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