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- PDB-1abo: CRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 D... -

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Basic information

Entry
Database: PDB / ID: 1abo
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 DOMAIN WITH 3BP-1 SYNTHETIC PEPTIDE
Components
  • 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES
  • ABL TYROSINE KINASE
KeywordsCOMPLEX (KINASE/PEPTIDE) / SH3 DOMAIN / TRANSFERASE (PHOSPHOTRANSFERASE) / PROTO-ONCOGENE / COMPLEX (KINASE-PEPTIDE) COMPLEX
Function / homology
Function and homology information


regulation of actin filament depolymerization / small GTPase binding => GO:0031267 / Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / negative regulation of small GTPase mediated signal transduction / RHO GTPases Activate WASPs and WAVEs / semaphorin receptor binding / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / transitional one stage B cell differentiation ...regulation of actin filament depolymerization / small GTPase binding => GO:0031267 / Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / negative regulation of small GTPase mediated signal transduction / RHO GTPases Activate WASPs and WAVEs / semaphorin receptor binding / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to epinephrine / regulation of cellular senescence / ruffle assembly / regulation of modification of synaptic structure / regulation of Rac protein signal transduction / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / Regulation of actin dynamics for phagocytic cup formation / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / regulation of blood vessel endothelial cell migration / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / Myogenesis / bubble DNA binding / cell junction assembly / filopodium assembly / activated T cell proliferation / establishment of epithelial cell apical/basal polarity / 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 / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / phagocytic cup / phagocytosis, engulfment / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / regulation of microtubule polymerization / B cell proliferation / positive regulation of osteoblast proliferation / cell leading edge / 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 / semaphorin-plexin signaling pathway / neuromuscular process controlling balance / platelet-derived growth factor receptor signaling pathway / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / endothelial cell migration / bicellular tight junction / positive regulation of T cell migration / canonical NF-kappaB signal transduction / BMP signaling pathway / phagocytosis / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / signal transduction in response to DNA damage / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / spleen development / ERK1 and ERK2 cascade / ruffle / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / actin filament polymerization / positive regulation of interleukin-2 production / phosphotyrosine residue binding / response to endoplasmic reticulum stress / SH2 domain binding / GTPase activator activity / ephrin receptor binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / post-embryonic development / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of endothelial cell migration
Similarity search - Function
BAR domain / BAR domain profile. / BAR / BAR domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / AH/BAR domain superfamily / Rho GTPase-activating protein domain ...BAR domain / BAR domain profile. / BAR / BAR domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1 / SH3 domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMusacchio, A. / Wilmanns, M. / Saraste, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides.
Authors: Musacchio, A. / Saraste, M. / Wilmanns, M.
#1: Journal: Embo J. / Year: 1993
Title: Crystal Structure of the SH3 Domain in Human Fyn. Comparison of the Three-Dimensional Structures of the SH3 Domain in Tyrosine Kinases and Spectrin
Authors: Noble, M.E.M. / Musacchio, A. / Courtneidge, S. / Saraste, M. / Wierenga, R.
#2: Journal: Science / Year: 1993
Title: Identification of a Ten-Amino Acid SH3 Binding Site
Authors: Ren, R. / Mayer, B. / Clark, K.L. / Baltimore, D.
#3: Journal: Nature / Year: 1992
Title: Crystal Structure of a Src-Homology 3 (SH3) Domain
Authors: Musacchio, A. / Noble, M.E.M. / Pauptit, R. / Wierenga, R. / Saraste, M.
History
DepositionMay 19, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: ABL TYROSINE KINASE
B: ABL TYROSINE KINASE
C: 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES
D: 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9886
Polymers15,7964
Non-polymers1922
Water2,180121
1
A: ABL TYROSINE KINASE
C: 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9943
Polymers7,8982
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-17 kcal/mol
Surface area4380 Å2
MethodPISA
2
B: ABL TYROSINE KINASE
D: 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9943
Polymers7,8982
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-17 kcal/mol
Surface area4440 Å2
MethodPISA
3
A: ABL TYROSINE KINASE
C: 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES
hetero molecules

B: ABL TYROSINE KINASE
D: 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9886
Polymers15,7964
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3190 Å2
ΔGint-61 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.800, 54.200, 35.000
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABL TYROSINE KINASE / P150


Mass: 6880.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P00520, EC: 2.7.1.112
#2: Protein/peptide 3BP-1 SYNTHETIC PEPTIDE, 10 RESIDUES


Mass: 1017.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: UniProt: P55194
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop / Details: used as seeds
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
210 mMTris1drop
3270 mM1dropNaCl
490 mMsodium citrate1reservoir
590 mMBis-Tris propane1reservoir
60.9 mMDTT1reservoir
70.9 mMEDTA1reservoir
80.9 mM1reservoirNaN3
938-42 %satammonium sulfate1reservoir
10lyophilized 3BP-2 peptide1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection% possible obs: 89 % / Rmerge(I) obs: 0.029
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.029

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.156 -
obs0.156 7499
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 10 121 1181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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