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- PDB-5c5b: Crystal Structure of Human APPL BAR-PH Heterodimer -

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Basic information

Entry
Database: PDB / ID: 5c5b
TitleCrystal Structure of Human APPL BAR-PH Heterodimer
Components
  • DCC-interacting protein 13-alpha
  • DCC-interacting protein 13-beta
KeywordsPROTEIN TRANSPORT / heterodimer
Function / homology
Function and homology information


negative regulation of cellular response to insulin stimulus / positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / early phagosome membrane / negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of fatty acid oxidation / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / negative regulation of neural precursor cell proliferation ...negative regulation of cellular response to insulin stimulus / positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / early phagosome membrane / negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of fatty acid oxidation / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / negative regulation of neural precursor cell proliferation / cold acclimation / 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 / positive regulation of phagocytosis, engulfment / negative regulation of D-glucose import / 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 / diet induced thermogenesis / beta-tubulin binding / regulation of G1/S transition of mitotic cell cycle / negative regulation of cytokine production involved in inflammatory response / regulation of protein localization to plasma membrane / ruffle / transforming growth factor beta receptor signaling pathway / phosphatidylinositol binding / positive regulation of D-glucose import / negative regulation of neurogenesis / ruffle membrane / protein import into nucleus / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / glucose homeostasis / presynapse / early endosome membrane / cytoplasmic vesicle / protein homotetramerization / 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. ...: / 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-beta / DCC-interacting protein 13-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsChen, Y.J. / Chen, B.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Hong Kong General Research FundHK-GRF 766911 Hong Kong
CitationJournal: To Be Published
Title: Crystal Structure of Human APPL BAR-PH Heterodimer
Authors: Chen, Y.J. / Chen, B.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DCC-interacting protein 13-alpha
B: DCC-interacting protein 13-beta
C: DCC-interacting protein 13-alpha
D: DCC-interacting protein 13-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,0787
Polymers170,8014
Non-polymers2763
Water41423
1
A: DCC-interacting protein 13-alpha
B: DCC-interacting protein 13-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5854
Polymers85,4012
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12180 Å2
ΔGint-100 kcal/mol
Surface area35390 Å2
MethodPISA
2
C: DCC-interacting protein 13-alpha
D: DCC-interacting protein 13-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4933
Polymers85,4012
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-101 kcal/mol
Surface area35040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.924, 88.542, 147.388
Angle α, β, γ (deg.)90.000, 92.650, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSchain AAA4 - 3754 - 375
21METMETLYSLYSchain CCC4 - 3754 - 375
12ASPASPSERSERchain BBB5 - 3745 - 374
22ASPASPARGARGchain DDD5 - 3755 - 375

NCS ensembles :
ID
1
2

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Components

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


Mass: 42966.359 Da / Num. of mol.: 2 / Fragment: BAR-PH domain, UNP residues 5-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APPL1, APPL, DIP13A, KIAA1428 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKG1
#2: Protein DCC-interacting protein 13-beta / Dip13-beta / Adapter protein containing PH domain / PTB domain and leucine zipper motif 2


Mass: 42434.359 Da / Num. of mol.: 2 / Fragment: UNP residues 1-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APPL2, DIP13B / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEU8
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M disodium hydrogen phosphate, 18% (w/v) PEG3350, 100 mM HEPES, and 1 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 28, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 46308 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.89
Reflection shellMean I/σ(I) obs: 1.72 / % possible all: 90.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-20000.95data scaling
HKL-20000.95data reduction
PHASER2.5.7phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.077 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 2155 5.19 %Random selection
Rwork0.2104 39398 --
obs0.2135 41553 98.56 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.14 Å2 / Biso mean: 68.2411 Å2 / Biso min: 21.88 Å2
Refinement stepCycle: final / Resolution: 2.9→49.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11308 0 18 23 11349
Biso mean--85.76 48.21 -
Num. residues----1457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511494
X-RAY DIFFRACTIONf_angle_d0.97115537
X-RAY DIFFRACTIONf_chiral_restr0.0381775
X-RAY DIFFRACTIONf_plane_restr0.0052030
X-RAY DIFFRACTIONf_dihedral_angle_d15.4024236
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3172X-RAY DIFFRACTION5.837TORSIONAL
12C3172X-RAY DIFFRACTION5.837TORSIONAL
21B3243X-RAY DIFFRACTION5.837TORSIONAL
22D3243X-RAY DIFFRACTION5.837TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.96750.34491450.29512572271796
2.9675-3.04170.35961560.29462618277499
3.0417-3.12390.34781560.28212576273299
3.1239-3.21580.38261610.2612608276999
3.2158-3.31960.35411450.25562621276699
3.3196-3.43820.31061250.24482669279499
3.4382-3.57580.29561400.23642644278499
3.5758-3.73850.2891410.22182634277599
3.7385-3.93550.31531290.20982628275799
3.9355-4.1820.24661380.19772635277399
4.182-4.50470.24331510.18122634278599
4.5047-4.95760.23821320.17862637276999
4.9576-5.67410.23651510.18942645279699
5.6741-7.14520.24161430.20726862829100
7.1452-49.08370.17861420.16082591273394

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