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- PDB-1i7a: EVH1 DOMAIN FROM MURINE HOMER 2B/VESL 2 -

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Basic information

Entry
Database: PDB / ID: 1i7a
TitleEVH1 DOMAIN FROM MURINE HOMER 2B/VESL 2
Components
  • HOMER 2B
  • PHE-ALA-PHE
KeywordsSIGNALING PROTEIN / EVH1 domain / Homer / Vesl / X-ray crystal structure / brain
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / Neurexins and neuroligins / intracellular organelle / synaptic receptor adaptor activity / stereocilium tip / regulation of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / behavioral response to cocaine ...G protein-coupled glutamate receptor binding / Neurexins and neuroligins / intracellular organelle / synaptic receptor adaptor activity / stereocilium tip / regulation of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / behavioral response to cocaine / sensory perception of sound / calcium-mediated signaling / apical part of cell / actin binding / postsynaptic density / glutamatergic synapse / 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
CITRATE ANION / PHENYLALANINE / Homer protein homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsBarzik, M. / Carl, U.D. / Schubert, W.-D. / Wehland, J. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The N-terminal domain of Homer/Vesl is a new class II EVH1 domain.
Authors: Barzik, M. / Carl, U.D. / Schubert, W.D. / Frank, R. / Wehland, J. / Heinz, D.W.
History
DepositionMar 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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

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Assembly

Deposited unit
A: HOMER 2B
B: HOMER 2B
C: HOMER 2B
D: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,56210
Polymers50,6885
Non-polymers8745
Water1,910106
1
A: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3144
Polymers12,9602
Non-polymers3542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9303
Polymers12,5761
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HOMER 2B


Theoretical massNumber of molelcules
Total (without water)12,5761
Polymers12,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7412
Polymers12,5761
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: HOMER 2B
hetero molecules

B: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0556
Polymers25,5363
Non-polymers5193
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_556-x,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-13 kcal/mol
Surface area10380 Å2
MethodPISA
6
A: HOMER 2B
hetero molecules

C: HOMER 2B


Theoretical massNumber of molelcules
Total (without water)25,5074
Polymers25,1522
Non-polymers3542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area2610 Å2
ΔGint-6 kcal/mol
Surface area10230 Å2
MethodPISA
7
C: HOMER 2B

A: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8905
Polymers25,5363
Non-polymers3542
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-11 kcal/mol
Surface area10290 Å2
MethodPISA
8
B: HOMER 2B
hetero molecules

D: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6725
Polymers25,1522
Non-polymers5193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area2650 Å2
ΔGint-7 kcal/mol
Surface area10320 Å2
MethodPISA
9
E: PHE-ALA-PHE


  • defined by software
  • 383 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3831
Polymers3831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
B: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3144
Polymers12,9602
Non-polymers3542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-6 kcal/mol
Surface area6350 Å2
MethodPISA
11
A: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9303
Polymers12,5761
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.716, 50.014, 73.098
Angle α, β, γ (deg.)90.00, 101.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HOMER 2B / HOMER 2B/VESL 2


Mass: 12576.193 Da / Num. of mol.: 4 / Fragment: EVH1 DOMAIN (N-TERMINAL)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: BRAIN / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON + / References: UniProt: Q9QWW1
#2: Protein/peptide PHE-ALA-PHE


Mass: 383.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M SODIUM CITRATE, O.1 M CHES, pH 9.8, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 55.3 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mammonium sulfate11
20.1 MHEPES11
310 mMNAD11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 59066 / Num. obs: 22446 / % possible obs: 95.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3 / Num. unique all: 2060 / % possible all: 88.2
Reflection shell
*PLUS
% possible obs: 88.2 % / Rmerge(I) obs: 0.28

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
REFMACrefinement
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDW (SAME MOLECULE IN DIFFERENT PACKING DERIVED FROM HOMER 1B FROM RAT

1ddw


Resolution: 2.24→15 Å / Isotropic thermal model: Isotropic / σ(F): 3 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: The crystal had a particularly high mosaicity.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 961 4.9 %random
Rwork0.235 ---
all-23487 --
obs-19460 85.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.77 Å21.19 Å20.23 Å2
2--0 Å2-0.89 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.24→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 60 108 3515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.186
X-RAY DIFFRACTIONp_bond_d0.068
LS refinement shellResolution: 2.2→2.24 Å
RfactorNum. reflection% reflection
Rfree0.35 26 -
Rwork0.25 --
obs-705 83.7 %
Software
*PLUS
Name: CNS/REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 4.9 % / Rfactor obs: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d

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