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

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Basic information

Entry
Database: PDB / ID: 6ovf
TitleCrystal Structure of the Disabled-2 (Dab2) Dab Homology Domain in Complex with Peptide STA03
Components
  • Disabled homolog 2
  • STA03
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 / positive regulation of Wnt signaling pathway, planar cell polarity pathway / clathrin coat assembly / clathrin-coated vesicle membrane / Formation of annular gap junctions ...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 / positive regulation of Wnt signaling pathway, planar cell polarity pathway / clathrin coat assembly / clathrin-coated vesicle membrane / Formation of annular gap junctions / Gap junction degradation / clathrin adaptor activity / response to salt / negative regulation of protein localization to plasma membrane / 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 / positive regulation of epithelial to mesenchymal transition / clathrin-coated pit / positive regulation of substrate adhesion-dependent cell spreading / cellular response to epidermal growth factor stimulus / transforming growth factor beta receptor signaling pathway / receptor-mediated endocytosis / negative regulation of protein binding / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / negative regulation of cell growth / fibrillar center / Wnt signaling pathway / negative regulation of epithelial cell proliferation / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / negative regulation of neuron projection development / Clathrin-mediated endocytosis / positive regulation of cell migration / positive regulation of protein phosphorylation / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm / cytosol
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: 1.95 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 STA03
Authors: Chavez, M. / Madden, D.R.
History
DepositionMay 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 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 / 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: STA03
D: STA03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1599
Polymers38,9684
Non-polymers1905
Water4,810267
1
A: Disabled homolog 2
C: STA03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6265
Polymers19,4842
Non-polymers1423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-16 kcal/mol
Surface area9220 Å2
MethodPISA
2
B: Disabled homolog 2
D: STA03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5334
Polymers19,4842
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-8 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.644, 102.644, 80.202
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-202-

MG

21A-385-

HOH

31A-406-

HOH

41B-353-

HOH

51B-359-

HOH

61B-372-

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 STA03


Mass: 1447.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM MgCl*6H2O, 5 mM Ni(II)Cl*6H2O, 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: BL9-2 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 1.95→19.85 Å / Num. obs: 35885 / % possible obs: 100 % / Redundancy: 10.92 % / Net I/σ(I): 23.04
Reflection shellResolution: 1.95→1.9757 Å / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 4.51 / Num. unique obs: 8485 / CC1/2: 0.927 / Rrim(I) all: 0.673 / % 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: 1.95→19.849 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.2069 3584 9.99 %
Rwork0.1754 --
obs0.1786 35884 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 5 267 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072699
X-RAY DIFFRACTIONf_angle_d0.7933616
X-RAY DIFFRACTIONf_dihedral_angle_d4.7132282
X-RAY DIFFRACTIONf_chiral_restr0.057374
X-RAY DIFFRACTIONf_plane_restr0.005480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97570.27521780.23351176X-RAY DIFFRACTION100
1.9757-2.00270.293850.21071281X-RAY DIFFRACTION100
2.0027-2.03130.2839950.21191256X-RAY DIFFRACTION100
2.0313-2.06160.2631780.21561192X-RAY DIFFRACTION100
2.0616-2.09370.2381840.18841192X-RAY DIFFRACTION100
2.0937-2.1280.2289640.19161265X-RAY DIFFRACTION100
2.128-2.16470.24011170.18421277X-RAY DIFFRACTION100
2.1647-2.2040.19771810.17231164X-RAY DIFFRACTION100
2.204-2.24630.2241810.17461200X-RAY DIFFRACTION100
2.2463-2.29210.20941190.17421251X-RAY DIFFRACTION100
2.2921-2.34190.1955640.17141302X-RAY DIFFRACTION100
2.3419-2.39630.19681780.16641191X-RAY DIFFRACTION100
2.3963-2.45610.19421780.17071189X-RAY DIFFRACTION100
2.4561-2.52240.21711620.18321200X-RAY DIFFRACTION100
2.5224-2.59640.2853200.17341365X-RAY DIFFRACTION100
2.5964-2.68010.21461780.17311195X-RAY DIFFRACTION100
2.6801-2.77560.21141820.18641217X-RAY DIFFRACTION100
2.7756-2.88640.21691800.17851193X-RAY DIFFRACTION100
2.8864-3.01731000000000.16521371X-RAY DIFFRACTION100
3.0173-3.17580.1981790.1641210X-RAY DIFFRACTION100
3.1758-3.37390.18481790.16451195X-RAY DIFFRACTION100
3.3739-3.63290.19631780.16011228X-RAY DIFFRACTION100
3.6329-3.99580.1907860.15641311X-RAY DIFFRACTION100
3.9958-4.56790.1919930.15991304X-RAY DIFFRACTION100
4.5679-5.7320.20051760.18451259X-RAY DIFFRACTION100
5.732-19.85010.20481690.20181316X-RAY DIFFRACTION100

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