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- PDB-3cve: Crystal Structure of the carboxy terminus of Homer1 -

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Basic information

Entry
Database: PDB / ID: 3cve
TitleCrystal Structure of the carboxy terminus of Homer1
ComponentsHomer protein homolog 1
KeywordsSIGNALING PROTEIN / coiled coil / Alternative splicing / Cell junction / Cytoplasm / Membrane / Postsynaptic cell membrane / Synapse
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 / neuron spine / G protein-coupled glutamate receptor signaling pathway / 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 / neuron spine / G protein-coupled glutamate receptor signaling pathway / costamere / positive regulation of calcium ion transport / type 5 metabotropic glutamate receptor binding / postsynaptic cytosol / behavioral response to cocaine / skeletal muscle contraction / excitatory synapse / skeletal muscle fiber development / regulation of synaptic transmission, glutamatergic / dendritic shaft / response to cocaine / response to nicotine / protein tetramerization / Z disc / response to calcium ion / circadian rhythm / apical part of cell / scaffold protein binding / transmembrane transporter binding / postsynapse / 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 / 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 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 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 1.2Jun 7, 2017Group: Refinement description
Revision 1.3Oct 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 1.4Oct 20, 2021Group: 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 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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 1
B: Homer protein homolog 1
C: Homer protein homolog 1
D: Homer protein homolog 1


Theoretical massNumber of molelcules
Total (without water)33,8574
Polymers33,8574
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-91.8 kcal/mol
Surface area16600 Å2
MethodPISA
2
A: Homer protein homolog 1
B: Homer protein homolog 1


Theoretical massNumber of molelcules
Total (without water)16,9282
Polymers16,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-16.4 kcal/mol
Surface area11430 Å2
MethodPISA
3
C: Homer protein homolog 1
D: Homer protein homolog 1


Theoretical massNumber of molelcules
Total (without water)16,9282
Polymers16,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-17 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.014, 62.508, 57.526
Angle α, β, γ (deg.)90.00, 102.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Homer protein homolog 1 / PSD-Zip45 / VASP/Ena-related gene up-regulated during seizure and LTP


Mass: 8464.209 Da / Num. of mol.: 4 / Fragment: Coiled-coil region, UNP residues 302-366 / Mutation: L308M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Homer1, Homer, Vesl / Plasmid: pET15a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z214
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 297 K / Method: hanging drop / pH: 6
Details: 0.1 M MES, 0.1 M ammonium sulfate, 16% PEG1000, 10% glycerol, pH 6.0, hanging drop, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9794,0.9801,0.9600
DetectorType: Quantum-4 ADSC / Detector: CCD / Date: Aug 12, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.98011
30.961
ReflectionResolution: 1.75→50 Å / Num. obs: 26705 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.75-1.813.10.19696.4
1.81-1.893.10.16298.4
1.89-1.973.80.1398.7
1.97-2.073.40.09599
2.07-2.23.40.08199.2
2.2-2.383.50.06899.5
2.38-2.613.50.06199.3
2.61-2.993.40.05499.6
2.99-3.773.40.04998.7
3.77-503.20.0590.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 1.75→7.97 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.882 / SU B: 3.638 / SU ML: 0.096 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.16
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1337 5 %RANDOM
Rwork0.216 ---
obs0.22 26692 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→7.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 0 269 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222156
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3022.0072870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6985257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97326.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01315487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4021516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021556
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.21158
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21536
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1021.51361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61922068
X-RAY DIFFRACTIONr_scbond_it3.3573875
X-RAY DIFFRACTIONr_scangle_it5.0744.5802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 93 -
Rwork0.231 1783 -
obs--97.2 %

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