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- PDB-2ela: Crystal Structure of the PTB domain of human APPL1 -

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Basic information

Entry
Database: PDB / ID: 2ela
TitleCrystal Structure of the PTB domain of human APPL1
ComponentsAdapter protein containing PH domain, PTB domain and leucine zipper motif 1
KeywordsCELL CYCLE / APPL / PTB 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 / regulation of glucose import / protein kinase B binding / 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 / regulation of glucose import / protein kinase B binding / maintenance of synapse structure / signaling / positive regulation of melanin biosynthetic process / regulation of toll-like receptor 4 signaling pathway / vesicle membrane / early phagosome / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of cytokine production involved in inflammatory response / cellular response to hepatocyte growth factor stimulus / intracellular vesicle / regulation of innate immune response / beta-tubulin binding / phosphatidylserine binding / regulation of G1/S transition of mitotic cell cycle / regulation of protein localization to plasma membrane / ruffle / phosphatidylinositol binding / transforming growth factor beta receptor signaling pathway / positive regulation of glucose import / protein import into nucleus / presynapse / insulin receptor signaling pathway / early endosome membrane / cytoplasmic vesicle / postsynapse / early endosome / endosome membrane / endosome / cell cycle / glutamatergic synapse / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
APPL1, BAR domain / : / : / : / BAR domain of APPL family / BAR domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain ...APPL1, BAR domain / : / : / : / BAR domain of APPL family / 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 / 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 / Mainly Beta
Similarity search - Domain/homology
DCC-interacting protein 13-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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


Theoretical massNumber of molelcules
Total (without water)39,8742
Polymers39,8742
Non-polymers00
Water4,252236
1
A: Adapter protein containing PH domain, PTB domain and leucine zipper motif 1


Theoretical massNumber of molelcules
Total (without water)19,9371
Polymers19,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adapter protein containing PH domain, PTB domain and leucine zipper motif 1


Theoretical massNumber of molelcules
Total (without water)19,9371
Polymers19,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.533, 61.593, 60.745
Angle α, β, γ (deg.)90.00, 101.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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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: 19936.799 Da / Num. of mol.: 2 / Fragment: PTB 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate (pH 5.6), 10% (w/v) PEG 10K, 10% (v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.97641
SYNCHROTRONNSLS X4C20.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 19, 2005
MAR scanner 180 mm plate2IMAGE PLATEJul 24, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976411
20.97951
ReflectionResolution: 2→30 Å / Num. obs: 23819 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.74
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.917 / Num. unique all: 2274 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 435558.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1557 7.3 %RANDOM
Rwork0.222 ---
obs0.222 21359 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6133 Å2 / ksol: 0.342706 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-8.74 Å20 Å2-0.81 Å2
2--0.07 Å20 Å2
3----8.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 0 236 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.692.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.307 133 6.9 %
Rwork0.262 1782 -
obs--86 %
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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