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- PDB-2ho2: Structure of human FE65-WW domain in complex with hMena peptide. -

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Basic information

Entry
Database: PDB / ID: 2ho2
TitleStructure of human FE65-WW domain in complex with hMena peptide.
Components
  • Amyloid beta A4 protein-binding family B member 1
  • Protein enabled homolog
KeywordsPROTEIN BINDING / WW DOMAIN / BETA SHEET / FE65
Function / homology
Function and homology information


actin polymerization-dependent cell motility / negative regulation of cell cycle G1/S phase transition / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / proline-rich region binding / low-density lipoprotein particle receptor binding / Generation of second messenger molecules / smooth muscle contraction ...actin polymerization-dependent cell motility / negative regulation of cell cycle G1/S phase transition / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / proline-rich region binding / low-density lipoprotein particle receptor binding / Generation of second messenger molecules / smooth muscle contraction / axonogenesis / filopodium / positive regulation of protein secretion / axon guidance / positive regulation of neuron projection development / SH3 domain binding / lamellipodium / cell junction / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / actin binding / amyloid-beta binding / histone binding / growth cone / molecular adaptor activity / transcription coactivator activity / cytoskeleton / nuclear speck / positive regulation of apoptotic process / focal adhesion / apoptotic process / ubiquitin protein ligase binding / synapse / DNA damage response / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Amyloid beta precursor protein binding family B member 1/2/3 / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. ...Amyloid beta precursor protein binding family B member 1/2/3 / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid beta precursor protein binding family B member 1 / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.33 Å
AuthorsMeiyappan, M. / Birrane, G. / Ladias, J.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for Polyproline Recognition by the FE65 WW Domain.
Authors: Meiyappan, M. / Birrane, G. / Ladias, J.A.
History
DepositionJul 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Amyloid beta A4 protein-binding family B member 1
B: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2923
Polymers5,2002
Non-polymers921
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.661, 41.661, 38.633
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-260-

MET

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Components

#1: Protein/peptide Amyloid beta A4 protein-binding family B member 1 / Fe65 protein


Mass: 4194.533 Da / Num. of mol.: 1 / Fragment: WW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: O00213
#2: Protein/peptide Protein enabled homolog / hMENA


Mass: 1005.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q8N8S7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.86 Å3/Da / Density % sol: 33.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.85M Ammonium Sulfate, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9792, 0.9793, 0.96
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2006 / Details: DUAL SLITS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97931
30.961
ReflectionResolution: 1.33→50 Å / Num. all: 9258 / Num. obs: 9129 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Χ2: 1.075 / Net I/σ(I): 23.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.33-1.385.40.4388151.161190.3
1.38-1.436.60.3489091.157198.7
1.43-1.56.60.2489021.136199.1
1.5-1.586.80.1569031.09199.3
1.58-1.686.70.1169001.09199.2
1.68-1.816.70.0799090.992199.7
1.81-1.996.70.0589241.049199.8
1.99-2.276.60.0519311.031100
2.27-2.876.60.0489370.984199.9
2.87-506.10.0519991.094199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.33→17.03 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.702 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 431 4.7 %RANDOM
Rwork0.172 ---
all0.174 9129 --
obs0.174 9085 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.478 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.33→17.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms339 0 6 34 379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022377
X-RAY DIFFRACTIONr_bond_other_d0.0020.02272
X-RAY DIFFRACTIONr_angle_refined_deg1.9582527
X-RAY DIFFRACTIONr_angle_other_deg1.0933667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.754545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.4522.30813
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2281542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.444152
X-RAY DIFFRACTIONr_chiral_restr0.1130.251
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0264
X-RAY DIFFRACTIONr_nbd_refined0.240.264
X-RAY DIFFRACTIONr_nbd_other0.2020.2230
X-RAY DIFFRACTIONr_nbtor_refined0.2010.2168
X-RAY DIFFRACTIONr_nbtor_other0.0960.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.27
X-RAY DIFFRACTIONr_mcbond_it2.571.5280
X-RAY DIFFRACTIONr_mcbond_other1.0741.580
X-RAY DIFFRACTIONr_mcangle_it3.0832385
X-RAY DIFFRACTIONr_scbond_it3.5143185
X-RAY DIFFRACTIONr_scangle_it3.8774.5140
X-RAY DIFFRACTIONr_rigid_bond_restr1.7843839
X-RAY DIFFRACTIONr_sphericity_free11.263334
X-RAY DIFFRACTIONr_sphericity_bonded6.0363628
LS refinement shellResolution: 1.33→1.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 42 -
Rwork0.213 588 -
obs-630 98.13 %

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