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- PDB-5dc0: CRYSTAL STRUCTURE OF MONOBODY GG3/ABL1 SH2 DOMAIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 5dc0
TitleCRYSTAL STRUCTURE OF MONOBODY GG3/ABL1 SH2 DOMAIN COMPLEX
Components
  • Fibronectin
  • Tyrosine-protein kinase ABL1
KeywordsPROTEIN BINDING / ENGINEERED BINDING PROTEIN / ANTIBODY MIMIC / PROTEIN-PROTEIN COMPLEX / SH2 DOMAIN / TYROSINE-PROTEIN KINASE
Function / homology
Function and homology information


negative regulation of monocyte activation / positive regulation of actin filament binding / negative regulation of transforming growth factor beta production / calcium-independent cell-matrix adhesion / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / negative regulation of ubiquitin-protein transferase activity / DN4 thymocyte differentiation / Extracellular matrix organization / Fibronectin matrix formation ...negative regulation of monocyte activation / positive regulation of actin filament binding / negative regulation of transforming growth factor beta production / calcium-independent cell-matrix adhesion / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / negative regulation of ubiquitin-protein transferase activity / DN4 thymocyte differentiation / Extracellular matrix organization / Fibronectin matrix formation / response to epinephrine / positive regulation of substrate-dependent cell migration, cell attachment to substrate / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / transitional one stage B cell differentiation / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / regulation of postsynaptic specialization assembly / neural crest cell migration involved in autonomic nervous system development / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / DNA conformation change / positive regulation of microtubule binding / peptidase activator activity / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / fibrinogen complex / positive regulation of extracellular matrix organization / microspike assembly / positive regulation of blood vessel branching / B-1 B cell homeostasis / peptide cross-linking / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / negative regulation of protein serine/threonine kinase activity / integrin activation / ALK mutants bind TKIs / activated T cell proliferation / positive regulation of establishment of T cell polarity / cellular response to dopamine / regulation of cell motility / cell-substrate junction assembly / proline-rich region binding / regulation of Cdc42 protein signal transduction / syntaxin binding / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / proteoglycan binding / myoblast proliferation / alpha-beta T cell differentiation / biological process involved in interaction with symbiont / positive regulation of dendrite development / regulation of T cell differentiation / extracellular matrix structural constituent / regulation of axon extension / cardiac muscle cell proliferation / Molecules associated with elastic fibres / MET activates PTK2 signaling / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Syndecan interactions / response to muscle activity / p130Cas linkage to MAPK signaling for integrins / Myogenesis / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of osteoblast proliferation / endodermal cell differentiation / RUNX2 regulates osteoblast differentiation / regulation of microtubule polymerization / endoplasmic reticulum-Golgi intermediate compartment / Fc-gamma receptor signaling pathway involved in phagocytosis / associative learning / Bergmann glial cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of endocytosis / neuromuscular process controlling balance / basement membrane / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / Non-integrin membrane-ECM interactions / negative regulation of cellular senescence / actin monomer binding / negative regulation of BMP signaling pathway / endothelial cell migration / positive regulation of focal adhesion assembly / signal transduction in response to DNA damage / canonical NF-kappaB signal transduction / RHO GTPases Activate WASPs and WAVEs / ECM proteoglycans / positive regulation of T cell migration / Integrin cell surface interactions / positive regulation of axon extension / BMP signaling pathway / regulation of cell adhesion
Similarity search - Function
Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain ...Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / SH2 domain / SHC Adaptor Protein / : / Kringle-like fold / Fibronectin type III domain / EGF-like domain signature 1. / SH3 domain / Fibronectin type 3 domain / SH2 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1 / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsWojcik, J.B. / Grabe, G. / Koide, S.
Funding support United States, Switzerland, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM090324 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM07281 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA014599 United States
Swiss Cancer LeagueS-3132-02-2013; KLS-3595-02-2015 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface.
Authors: Wojcik, J. / Lamontanara, A.J. / Grabe, G. / Koide, A. / Akin, L. / Gerig, B. / Hantschel, O. / Koide, S.
History
DepositionAug 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibronectin
B: Tyrosine-protein kinase ABL1


Theoretical massNumber of molelcules
Total (without water)23,4382
Polymers23,4382
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-2 kcal/mol
Surface area10110 Å2
Unit cell
Length a, b, c (Å)131.437, 37.348, 39.705
Angle α, β, γ (deg.)90.00, 98.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 9866.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02751*PLUS
#2: Protein Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1 / Proto- ...Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1 / Proto-oncogene c-Abl / p150


Mass: 13571.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M sodium tartrate pH=8 and 25% w/v polyethylene glycol 3350
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2010
RadiationMonochromator: SI 111 SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.23→65.01 Å / Num. obs: 9392 / % possible obs: 98.7 % / Redundancy: 4.4 % / Net I/σ(I): 17.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→65.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.852 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24386 448 4.8 %RANDOM
Rwork0.19129 ---
obs0.1938 8914 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.722 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.03 Å2
2---0.26 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.23→65.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 0 55 1518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021503
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9452057
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5722.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94515223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.394158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211137
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.234→2.292 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 33 -
Rwork0.218 556 -
obs--88.84 %

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