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- PDB-4h8s: Crystal structure of human APPL2BARPH domain -

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Basic information

Entry
Database: PDB / ID: 4h8s
TitleCrystal structure of human APPL2BARPH domain
ComponentsDCC-interacting protein 13-beta
KeywordsSIGNALING PROTEIN / BAR domain / pleckstrin homology domain / adaptor protein / Rab binding
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 fatty acid oxidation / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / cold acclimation / 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 fatty acid oxidation / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / cold acclimation / negative regulation of neural precursor cell proliferation / signaling / regulation of toll-like receptor 4 signaling pathway / positive regulation of phagocytosis, engulfment / negative regulation of glucose import / early phagosome / cellular response to hepatocyte growth factor stimulus / regulation of innate immune response / phosphatidylserine binding / diet induced thermogenesis / regulation of G1/S transition of mitotic cell cycle / negative regulation of cytokine production involved in inflammatory response / ruffle / phosphatidylinositol binding / transforming growth factor beta receptor signaling pathway / ruffle membrane / negative regulation of neurogenesis / protein import into nucleus / glucose homeostasis / positive regulation of cold-induced thermogenesis / early endosome membrane / cytoplasmic vesicle / protein homotetramerization / vesicle / endosome membrane / endosome / cell cycle / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
: / : / : / : / 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 ...: / : / : / : / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMartin, J.L. / King, G.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Membrane Curvature Protein Exhibits Interdomain Flexibility and Binds a Small GTPase.
Authors: King, G.J. / Stockli, J. / Hu, S.H. / Winnen, B. / Duprez, W.G. / Meoli, C.C. / Junutula, J.R. / Jarrott, R.J. / James, D.E. / Whitten, A.E. / Martin, J.L.
History
DepositionSep 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)184,4854
Polymers184,4854
Non-polymers00
Water00
1
A: DCC-interacting protein 13-beta
B: DCC-interacting protein 13-beta


Theoretical massNumber of molelcules
Total (without water)92,2422
Polymers92,2422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-88 kcal/mol
Surface area38740 Å2
MethodPISA
2
C: DCC-interacting protein 13-beta
D: DCC-interacting protein 13-beta


Theoretical massNumber of molelcules
Total (without water)92,2422
Polymers92,2422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-90 kcal/mol
Surface area39010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.960, 208.013, 218.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DCC-interacting protein 13-beta / APPL2BARPH / Dip13-beta / Adapter protein containing PH domain / PTB domain and leucine zipper motif 2


Mass: 46121.219 Da / Num. of mol.: 4 / Fragment: UNP residues 2-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APPL2, DIP13B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NEU8

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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: 6.01 Å3/Da / Density % sol: 79.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.9% w/v PEG8000, 40 mM hexamine cobalt(III) chloride, 20% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953698 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953698 Å / Relative weight: 1
ReflectionResolution: 3.5→46.95 Å / Num. obs: 55792 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 98 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 11.3
Reflection shellHighest resolution: 3.5 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1031)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q13

2q13


Resolution: 3.5→46.95 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 2806 5.16 %RANDOM
Rwork0.2092 ---
obs0.2116 54413 95.38 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 128 Å2
Refinement stepCycle: LAST / Resolution: 3.5→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11958 0 0 0 11958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512128
X-RAY DIFFRACTIONf_angle_d0.97616337
X-RAY DIFFRACTIONf_dihedral_angle_d14.844623
X-RAY DIFFRACTIONf_chiral_restr0.0521841
X-RAY DIFFRACTIONf_plane_restr0.0032130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.56030.37931260.30122246X-RAY DIFFRACTION85
3.5603-3.62510.34461110.28182319X-RAY DIFFRACTION86
3.6251-3.69480.33471140.27772366X-RAY DIFFRACTION89
3.6948-3.77010.30731440.26352447X-RAY DIFFRACTION91
3.7701-3.85210.25961100.24162451X-RAY DIFFRACTION92
3.8521-3.94160.31911230.23122479X-RAY DIFFRACTION92
3.9416-4.04020.28211650.22162510X-RAY DIFFRACTION94
4.0402-4.14930.26121480.20842550X-RAY DIFFRACTION96
4.1493-4.27140.27181570.20382604X-RAY DIFFRACTION97
4.2714-4.40910.25211300.19082596X-RAY DIFFRACTION97
4.4091-4.56660.24061640.18232599X-RAY DIFFRACTION98
4.5666-4.74930.23451450.18092648X-RAY DIFFRACTION98
4.7493-4.96520.26631520.1662646X-RAY DIFFRACTION98
4.9652-5.22660.23041510.17572675X-RAY DIFFRACTION99
5.2266-5.55360.25561490.19692651X-RAY DIFFRACTION98
5.5536-5.98160.26631360.22782683X-RAY DIFFRACTION98
5.9816-6.58210.26041280.23842730X-RAY DIFFRACTION99
6.5821-7.53120.26721540.22142746X-RAY DIFFRACTION100
7.5312-9.47570.22891610.18182745X-RAY DIFFRACTION100
9.4757-46.95370.20631380.20942916X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61720.0227-0.46261.81660.70970.2490.3685-0.0686-0.025-0.2674-0.46090.165-0.1665-0.07680.07580.93540.1123-0.13680.6244-0.06340.851819.7881-53.5348-67.9183
21.7057-1.7413-1.57961.9691.77671.36010.2249-0.05470.4174-0.11070.2168-0.5421-0.1541-0.1076-0.49220.89220.0309-0.04640.7956-0.06540.933818.9487-46.9403-66.624
34.16651.44340.96395.7022.15845.86990.29630.3094-0.0533-0.2275-0.10160.11220.3218-0.3226-0.1730.60190.0225-0.09830.7047-0.12440.7504-28.446510.873-38.8714
44.0887-4.6077-3.26628.89453.02691.53450.011-0.5530.2671-0.24220.4207-0.1503-0.05690.2812-0.43030.82190.1136-0.31650.7279-0.22130.7073.2379-35.9715-52.518
52.4742-1.9582-1.25651.83751.08430.5865-0.2297-0.15080.24390.41670.234-0.28450.19140.1318-0.0040.94860.0613-0.1170.8152-0.13080.85643.58-36.0381-51.0453
64.639-0.99890.15232.83460.02393.2477-0.12241.04330.05340.00430.104-0.56810.44140.230.13521.26030.2623-0.15731.0361-0.15980.694128.0738-91.0726-104.1859
71.1784-0.08490.59862.5131-2.76583.7944-0.32320.1024-0.62581.45710.63691.29851.2999-1.14280.03471.6213-0.04270.21151.5051-0.51340.9907-3.202514.819124.4122
81.1491-1.4451-1.35832.20032.44341.64990.19150.2349-0.0123-0.5284-0.33290.1832-0.4995-0.52030.24811.1214-0.01660.061.0834-0.18090.75066.648313.2198-6.3857
91.0989-0.1923-1.22221.20071.02832.2883-0.69570.0862-0.53650.6672-0.18640.36021.1313-0.34221.01670.6962-0.0335-0.05780.8150.070.564916.3845-5.7771-14.8504
103.40750.68640.85375.94520.52254.5514-0.01240.12840.2457-0.6693-0.1999-0.3559-0.27040.0250.22130.8478-0.03290.15520.9338-0.0560.683149.4806-11.5631-71.5797
115.40342.4396-3.14833.9824-4.07924.32590.2039-0.1008-0.4316-0.72680.07770.84330.04440.0899-0.050.9739-0.19490.06211.0644-0.08240.863842.7098-21.6215-53.5086
122.4012-1.7812-1.7041.08471.64652.2888-0.1558-0.37140.00090.13190.09630.0432-0.31190.118-0.04980.7948-0.08380.03720.7504-0.14920.617530.0963-5.7009-22.4597
132.3883-1.1927-2.2750.89331.33363.101-0.60760.0527-0.24730.32710.07660.27260.7536-0.26380.73560.727-0.0373-0.02580.6105-0.14780.755118.2248-2.7937-15.5771
144.01520.7012-1.32933.7668-1.21143.42230.0508-0.23070.64641.3813-0.14460.83150.9018-0.33310.0221.3745-0.17480.2230.8591-0.28110.9594-0.443143.456535.0439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain A and resid -4:81 )A-4 - 81
2X-RAY DIFFRACTION2( chain A and resid 82:264 )A82 - 264
3X-RAY DIFFRACTION3( chain A and resid 265:377 )A265 - 377
4X-RAY DIFFRACTION4( chain B and resid 7:82 )B7 - 82
5X-RAY DIFFRACTION5( chain B and resid 83:265 )B83 - 265
6X-RAY DIFFRACTION6( chain B and resid 266:378 )B266 - 378
7X-RAY DIFFRACTION7( chain C and resid -6:18 )C-6 - 18
8X-RAY DIFFRACTION8( chain C and resid 19:163 )C19 - 163
9X-RAY DIFFRACTION9( chain C and resid 164:264 )C164 - 264
10X-RAY DIFFRACTION10( chain C and resid 265:378 )C265 - 378
11X-RAY DIFFRACTION11( chain D and resid 5:18 )D5 - 18
12X-RAY DIFFRACTION12( chain D and resid 19:153 )D19 - 153
13X-RAY DIFFRACTION13( chain D and resid 154:271 )D154 - 271
14X-RAY DIFFRACTION14( chain D and resid 272:377 )D272 - 377

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