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- PDB-6o5o: Crystal Structure of the Disabled-2 (Dab2) Dab Homology Domain in... -

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Basic information

Entry
Database: PDB / ID: 6o5o
TitleCrystal Structure of the Disabled-2 (Dab2) Dab Homology Domain in Complex with Peptide STA02
Components
  • ACE-QNGFDNPNYQPQENMQA
  • Disabled homolog 2
KeywordsENDOCYTOSIS / Peptide Binding / Peptide Inhibitor / Protein-protein Interaction
Function / homology
Function and homology information


leading edge cell differentiation / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / positive regulation of clathrin-dependent endocytosis / positive regulation of early endosome to late endosome transport / negative regulation of androgen receptor signaling pathway / clathrin coat assembly / clathrin-coated vesicle membrane / positive regulation of Wnt signaling pathway, planar cell polarity pathway / clathrin adaptor activity ...leading edge cell differentiation / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / positive regulation of clathrin-dependent endocytosis / positive regulation of early endosome to late endosome transport / negative regulation of androgen receptor signaling pathway / clathrin coat assembly / clathrin-coated vesicle membrane / positive regulation of Wnt signaling pathway, planar cell polarity pathway / clathrin adaptor activity / Formation of annular gap junctions / Gap junction degradation / response to salt / response to steroid hormone / cargo receptor activity / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / SMAD binding / positive regulation of endocytosis / positive regulation of SMAD protein signal transduction / negative regulation of protein localization to plasma membrane / positive regulation of epithelial to mesenchymal transition / positive regulation of substrate adhesion-dependent cell spreading / clathrin-coated pit / cellular response to epidermal growth factor stimulus / receptor-mediated endocytosis / transforming growth factor beta receptor signaling pathway / negative regulation of protein binding / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / fibrillar center / negative regulation of epithelial cell proliferation / protein transport / negative regulation of neuron projection development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cell migration / positive regulation of protein phosphorylation / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Disabled homolog 2-like, sulfatide-binding motifs / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...: / : / Disabled homolog 2-like, sulfatide-binding motifs / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Disabled homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChavez, M. / Madden, D.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK104847 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK-117469 United States
CitationJournal: To Be Published
Title: Crystal Structure of the Disabled-2 (Dab2) Dab Homology Domain in Complex with Peptide STA02
Authors: Chavez, M. / Madden, D.R.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disabled homolog 2
B: Disabled homolog 2
C: ACE-QNGFDNPNYQPQENMQA
D: ACE-QNGFDNPNYQPQENMQA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,39910
Polymers40,1154
Non-polymers2836
Water6,179343
1
A: Disabled homolog 2
C: ACE-QNGFDNPNYQPQENMQA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2586
Polymers20,0582
Non-polymers2004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9 kcal/mol
Surface area9330 Å2
MethodPISA
2
B: Disabled homolog 2
D: ACE-QNGFDNPNYQPQENMQA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1414
Polymers20,0582
Non-polymers832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-10 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.724, 102.724, 80.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-201-

NI

21A-366-

HOH

31B-336-

HOH

41B-372-

HOH

51B-392-

HOH

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Components

#1: Protein Disabled homolog 2 / Adaptor molecule disabled-2 / Differentially expressed in ovarian carcinoma 2 / DOC-2 / ...Adaptor molecule disabled-2 / Differentially expressed in ovarian carcinoma 2 / DOC-2 / Differentially-expressed protein 2


Mass: 18036.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAB2, DOC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P98082
#2: Protein/peptide ACE-QNGFDNPNYQPQENMQA


Mass: 2021.084 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.07 Å3/Da / Density % sol: 59.92 % / Description: planar trapezoids, or hexagons
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM MgCl, 5 mM Ni(II)Cl, 0.1 M HEPES pH 7.0, 18% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.75→19.942 Å / Num. obs: 49944 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 22.4 Å2 / CC1/2: 1 / Rrim(I) all: 0.069 / Net I/σ(I): 29.77
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 4.55 / Num. unique obs: 9990 / CC1/2: 0.925 / Rrim(I) all: 0.721 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M7E

1m7e


Resolution: 1.75→19.942 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 2534 5.07 %
Rwork0.1727 --
obs0.174 49941 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→19.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 6 343 2935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082757
X-RAY DIFFRACTIONf_angle_d0.9613708
X-RAY DIFFRACTIONf_dihedral_angle_d20.7931098
X-RAY DIFFRACTIONf_chiral_restr0.069379
X-RAY DIFFRACTIONf_plane_restr0.006497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78370.25541260.2252604X-RAY DIFFRACTION100
1.7837-1.82010.26011240.21332623X-RAY DIFFRACTION100
1.8201-1.85960.26651260.20672645X-RAY DIFFRACTION100
1.8596-1.90280.25821260.19642604X-RAY DIFFRACTION100
1.9028-1.95040.22191280.18642629X-RAY DIFFRACTION100
1.9504-2.00310.21882510.18742478X-RAY DIFFRACTION100
2.0031-2.0620.21320.18382621X-RAY DIFFRACTION100
2.062-2.12840.20911300.17842636X-RAY DIFFRACTION100
2.1284-2.20440.21471290.17162614X-RAY DIFFRACTION100
2.2044-2.29260.21121280.17662653X-RAY DIFFRACTION100
2.2926-2.39670.21711310.16982619X-RAY DIFFRACTION100
2.3967-2.52290.19441240.17642642X-RAY DIFFRACTION100
2.5229-2.68060.18181280.17592646X-RAY DIFFRACTION100
2.6806-2.8870.20711280.18952653X-RAY DIFFRACTION100
2.887-3.17650.21391270.17822661X-RAY DIFFRACTION100
3.1765-3.63370.18292530.15792562X-RAY DIFFRACTION100
3.6337-4.5690.13711240.14682697X-RAY DIFFRACTION100
4.569-19.94280.23991190.16892820X-RAY DIFFRACTION100

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