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- PDB-3cvf: Crystal Structure of the carboxy terminus of Homer3 -

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Basic information

Entry
Database: PDB / ID: 3cvf
TitleCrystal Structure of the carboxy terminus of Homer3
ComponentsHomer protein homolog 3
KeywordsSIGNALING PROTEIN / coiled coil / Alternative splicing / Cell junction / Cytoplasm / Membrane / Phosphoprotein / Polymorphism / Postsynaptic cell membrane / Synapse
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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1700 / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Homer protein homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHayashi, M.K. / Stearns, M.H. / Giannini, V. / Xu, R.-M. / Sala, C. / Hayashi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: The postsynaptic density proteins Homer and Shank form a polymeric network structure.
Authors: Hayashi, M.K. / Tang, C. / Verpelli, C. / Narayanan, R. / Stearns, M.H. / Xu, R.M. / Li, H. / Sala, C. / Hayashi, Y.
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 40 MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ... MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,V.B.CHEN, : R.M.IMMORMINO,J.J.HEADD,W.B.ARENDALL,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK, : G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL, : J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON REFERENCE : MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE : VALIDATION FOR PROTEINS AND NUCLEIC ACIDS : NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homer protein homolog 3
B: Homer protein homolog 3
C: Homer protein homolog 3
D: Homer protein homolog 3


Theoretical massNumber of molelcules
Total (without water)36,2514
Polymers36,2514
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-87.4 kcal/mol
Surface area19020 Å2
MethodPISA
2
C: Homer protein homolog 3
D: Homer protein homolog 3


Theoretical massNumber of molelcules
Total (without water)18,1252
Polymers18,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-19.6 kcal/mol
Surface area12510 Å2
MethodPISA
3
A: Homer protein homolog 3
B: Homer protein homolog 3


Theoretical massNumber of molelcules
Total (without water)18,1252
Polymers18,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-16.8 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.029, 172.029, 66.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 9062.721 Da / Num. of mol.: 4 / Fragment: Coiled-coil region, residues 287-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOMER3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NSC5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 7.83 Å3/Da / Density % sol: 84.29 %
Crystal growTemperature: 297 K / Method: hanging drop / pH: 7.6
Details: 0.1 M Tris, 4.2 M NaCl, 10% glycerol, pH 7.6, hanging drop, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9795 Å
DetectorType: Quantum-4 ADSC / Detector: CCD / Date: Nov 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25036 / % possible obs: 99.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.9-35.60.25598.1
3-3.125.90.23599.4
3.12-3.276.10.16299.3
3.27-3.446.30.10799.3
3.44-3.656.70.09799.8
3.65-3.947.40.08699.7
3.94-4.338.10.078100
4.33-4.968.70.067100
4.96-6.248.70.069100
6.24-508.20.04498.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CVE

3cve


Resolution: 2.9→19.73 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.265
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28698 1269 5.1 %RANDOM
Rwork0.2522 ---
obs0.25391 23703 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 0 18 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212303
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3121.9853070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1055282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72323.475141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.37215452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7131542
X-RAY DIFFRACTIONr_chiral_restr0.1670.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2960.21042
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21523
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3520.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6031.51421
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.34522231
X-RAY DIFFRACTIONr_scbond_it3.3263874
X-RAY DIFFRACTIONr_scangle_it5.6824.5839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 95 -
Rwork0.338 1688 -
obs--98.18 %

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