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- PDB-3t04: Crystal structure of monobody 7c12/abl1 sh2 domain complex -

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Basic information

Entry
Database: PDB / ID: 3t04
TitleCrystal structure of monobody 7c12/abl1 sh2 domain complex
Components
  • MONOBODY 7C12
  • Tyrosine-protein kinase ABL1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / ENGINEERED BINDING PROTEIN / ANTIBODY MIMIC / PROTEIN-PROTEIN COMPLEX / SH2 DOMAIN / ATP-BINDING / PHOSPHOPROTEIN / TYROSINE-PROTEIN KINASE / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation ...: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / Bergmann glial cell differentiation / associative learning / neuromuscular process controlling balance / regulation of endocytosis / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / actin monomer binding / negative regulation of long-term synaptic potentiation / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / mismatch repair / BMP signaling pathway / regulation of cell adhesion / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / spleen development / ruffle / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / actin filament polymerization / phosphotyrosine residue binding / SH2 domain binding / response to endoplasmic reticulum stress / ephrin receptor binding / positive regulation of endothelial cell migration / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWojcik, J.B. / Wyrzucki, A.M. / Koide, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Targeting the SH2-Kinase Interface in Bcr-Abl Inhibits Leukemogenesis.
Authors: Grebien, F. / Hantschel, O. / Wojcik, J. / Kaupe, I. / Kovacic, B. / Wyrzucki, A.M. / Gish, G.D. / Cerny-Reiterer, S. / Koide, A. / Beug, H. / Pawson, T. / Valent, P. / Koide, S. / Superti-Furga, G.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
D: MONOBODY 7C12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4667
Polymers25,0012
Non-polymers4645
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-20 kcal/mol
Surface area11220 Å2
MethodPISA
2
A: Tyrosine-protein kinase ABL1
hetero molecules

D: MONOBODY 7C12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4667
Polymers25,0012
Non-polymers4645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area1050 Å2
ΔGint-22 kcal/mol
Surface area12340 Å2
MethodPISA
3
A: Tyrosine-protein kinase ABL1
hetero molecules

D: MONOBODY 7C12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4667
Polymers25,0012
Non-polymers4645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area2170 Å2
ΔGint-18 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.336, 49.396, 107.354
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 Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Proto-oncogene c-Abl / p150


Mass: 13715.132 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN (UNP RESIDUES 112-232)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL, ABL1, JTK7 / Plasmid: PHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Protein MONOBODY 7C12


Mass: 11286.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growpH: 6
Details: 0.2M MG(NO3)2, 100MM LICL, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2010
RadiationMonochromator: SI 111 SIDE BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 12700 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rsym value: 0.133 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OPK: 154-235, 1FNF: LOOPS OMITTED

1opk

1fnf


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.957 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 617 4.9 %RANDOM
Rwork0.19 ---
obs0.193 11957 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å2-0 Å2-0 Å2
2---0.85 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 29 127 1736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211652
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9592249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3722.67671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00815238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.743159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211268
X-RAY DIFFRACTIONr_mcbond_it0.9851.51000
X-RAY DIFFRACTIONr_mcangle_it1.82421623
X-RAY DIFFRACTIONr_scbond_it2.2833652
X-RAY DIFFRACTIONr_scangle_it3.7384.5626
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 48 -
Rwork0.214 805 -
obs--92.42 %

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