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- PDB-2elb: Crystal Structure of the BAR-PH domain of human APPL1 -

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Basic information

Entry
Database: PDB / ID: 2elb
TitleCrystal Structure of the BAR-PH domain of human APPL1
ComponentsAdapter protein containing PH domain, PTB domain and leucine zipper motif 1
KeywordsPROTEIN BINDING / APPL / BAR domain / PH domain
Function / homology
Function and homology information


negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / protein kinase B binding / regulation of D-glucose import / maintenance of synapse structure / signaling / positive regulation of melanin biosynthetic process ...negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / protein kinase B binding / regulation of D-glucose import / maintenance of synapse structure / signaling / positive regulation of melanin biosynthetic process / regulation of toll-like receptor 4 signaling pathway / early phagosome / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of cytokine production involved in inflammatory response / vesicle membrane / cellular response to hepatocyte growth factor stimulus / intracellular vesicle / regulation of innate immune response / phosphatidylserine binding / beta-tubulin binding / regulation of G1/S transition of mitotic cell cycle / regulation of protein localization to plasma membrane / ruffle / transforming growth factor beta receptor signaling pathway / phosphatidylinositol binding / positive regulation of D-glucose import / protein import into nucleus / insulin receptor signaling pathway / presynapse / early endosome membrane / cytoplasmic vesicle / postsynapse / early endosome / endosome membrane / endosome / glutamatergic synapse / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
APPL1, BAR domain / : / : / : / BAR domain of APPL family / Arfaptin homology (AH) domain/BAR domain / BAR domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain ...APPL1, BAR domain / : / : / : / BAR domain of APPL family / Arfaptin homology (AH) domain/BAR domain / BAR domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DCC-interacting protein 13-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLi, J. / Mao, X. / Dong, L.Q. / Liu, F. / Tong, L.
CitationJournal: Structure / Year: 2007
Title: Crystal Structures of the BAR-PH and PTB Domains of Human APPL1
Authors: Li, J. / Mao, X. / Dong, L.Q. / Liu, F. / Tong, L.
History
DepositionMar 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adapter protein containing PH domain, PTB domain and leucine zipper motif 1


Theoretical massNumber of molelcules
Total (without water)45,9871
Polymers45,9871
Non-polymers00
Water00
1
A: Adapter protein containing PH domain, PTB domain and leucine zipper motif 1

A: Adapter protein containing PH domain, PTB domain and leucine zipper motif 1


Theoretical massNumber of molelcules
Total (without water)91,9742
Polymers91,9742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11900 Å2
ΔGint-114 kcal/mol
Surface area35350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.568, 104.126, 37.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer.

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Components

#1: Protein Adapter protein containing PH domain, PTB domain and leucine zipper motif 1 / APPL1 / Dip13 alpha / DCC-interacting protein 13 alpha


Mass: 45987.117 Da / Num. of mol.: 1 / Fragment: The BAR-PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKG1

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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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 22% (w/v) polyacrylic acid 5100, 20mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 22741 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 27.5853
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 5.94 / Num. unique all: 2267 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.84 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 594181.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1429 7.4 %RANDOM
Rwork0.236 ---
obs0.236 19364 83.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.6318 Å2 / ksol: 0.304871 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---18.34 Å20 Å2
3---19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 0 0 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.329 109 8.7 %
Rwork0.287 1145 -
obs--54.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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