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- PDB-1bbz: CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED... -

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Basic information

Entry
Database: PDB / ID: 1bbz
TitleCRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED HIGH-AFFINITY PEPTIDE LIGAND: IMPLICATIONS FOR SH3-LIGAND INTERACTIONS
Components
  • ABL TYROSINE KINASE
  • PEPTIDE P41
KeywordsCOMPLEX (TRANSFERASE/PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) / SIGNAL TRANSDUCTION / SH3 DOMAIN / COMPLEX (TRANSFERASE-PEPTIDE) complex
Function / homology
Function and homology information


mitochondrial depolarization / positive regulation of interleukin-2 production => GO:0032743 / positive regulation of actin filament binding / transitional one stage B cell differentiation / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity ...mitochondrial depolarization / positive regulation of interleukin-2 production => GO:0032743 / positive regulation of actin filament binding / transitional one stage B cell differentiation / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity / alpha-beta T cell differentiation / B cell proliferation involved in immune response / regulation of modification of synaptic structure / positive regulation of microtubule binding / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / neuroepithelial cell differentiation / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / actin filament branching / positive regulation of oxidoreductase activity / activated T cell proliferation / circulatory system development => GO:0072359 / neuropilin binding / neuropilin signaling pathway / bubble DNA binding / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / regulation of T cell differentiation / negative regulation of ubiquitin-protein transferase activity / regulation of microtubule polymerization / negative regulation of BMP signaling pathway / regulation of actin cytoskeleton reorganization / mitogen-activated protein kinase binding / positive regulation of interferon-gamma production => GO:0032729 / proline-rich region binding / syntaxin binding / cellular response to dopamine / DNA damage induced protein phosphorylation / positive regulation of osteoblast proliferation / negative regulation of cell-cell adhesion / negative regulation of cellular senescence / regulation of response to DNA damage stimulus / regulation of axon extension / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of cell migration involved in sprouting angiogenesis / cell leading edge / negative regulation of long-term synaptic potentiation / actin monomer binding / neuromuscular process controlling balance / Bergmann glial cell differentiation / positive regulation of focal adhesion assembly / regulation of endocytosis / positive regulation of actin cytoskeleton reorganization / mismatch repair / regulation of hematopoietic stem cell differentiation / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / regulation of cell motility / negative regulation of mitotic cell cycle / positive regulation of substrate adhesion-dependent cell spreading / endothelial cell migration / positive regulation of muscle cell differentiation / four-way junction DNA binding / positive regulation of stress fiber assembly / signal transduction in response to DNA damage / regulation of actin cytoskeleton organization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / sequence-specific double-stranded DNA binding / regulation of autophagy / cellular protein modification process / spleen development / negative regulation of I-kappaB kinase/NF-kappaB signaling / post-embryonic development / positive regulation of mitotic cell cycle / positive regulation of release of sequestered calcium ion into cytosol / SH2 domain binding / negative regulation of ERK1 and ERK2 cascade / thymus development / phosphotyrosine residue binding / protein kinase C binding / neural tube closure / ephrin receptor binding / integrin-mediated signaling pathway / peptidyl-tyrosine autophosphorylation / actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / establishment of protein localization / SH3 domain binding / autophagy / postsynapse / cell cycle arrest / epidermal growth factor receptor signaling pathway / cellular response to hydrogen peroxide / positive regulation of neuron death / B cell receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis
Serine-threonine/tyrosine-protein kinase, catalytic domain / SH2 domain superfamily / Protein kinase-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Tyrosine-protein kinase ABL, SH2 domain / Tyrosine-protein kinase, active site / SH3 domain / SH3-like domain superfamily / Protein kinase, ATP binding site ...Serine-threonine/tyrosine-protein kinase, catalytic domain / SH2 domain superfamily / Protein kinase-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Tyrosine-protein kinase ABL, SH2 domain / Tyrosine-protein kinase, active site / SH3 domain / SH3-like domain superfamily / Protein kinase, ATP binding site / F-actin binding / SH2 domain / SH3 domain / Protein kinase domain / SH3 Domains / SH3 type barrels. / Roll / Mainly Beta
Tyrosine-protein kinase ABL1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPisabarro, M.T. / Serrano, L. / Wilmanns, M.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions.
Authors: Pisabarro, M.T. / Serrano, L. / Wilmanns, M.
#1: Journal: Biochemistry / Year: 1996
Title: Rational Design of Specific High-Affinity Peptide Ligands for the Abl-SH3 Domain
Authors: Pisabarro, M.T. / Serrano, L.
#2: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 28, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABL TYROSINE KINASE
B: PEPTIDE P41
C: ABL TYROSINE KINASE
D: PEPTIDE P41
E: ABL TYROSINE KINASE
F: PEPTIDE P41
G: ABL TYROSINE KINASE
H: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,21712
Polymers29,8338
Non-polymers3844
Water4,846269
1
A: ABL TYROSINE KINASE
B: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-24 kcal/mol
Surface area4020 Å2
MethodPISA
2
C: ABL TYROSINE KINASE
D: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-27 kcal/mol
Surface area4040 Å2
MethodPISA
3
E: ABL TYROSINE KINASE
F: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-27 kcal/mol
Surface area3960 Å2
MethodPISA
4
G: ABL TYROSINE KINASE
H: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-27 kcal/mol
Surface area4020 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)46.680, 73.790, 80.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.997724, -0.067192, 0.005638), (0.011972, 0.094239, -0.995478), (0.066357, 0.993279, 0.094829)13.597, 53.0221, -22.2311
2given(0.999017, -0.043051, -0.010579), (-0.010289, 0.006953, -0.999923), (0.043121, 0.999049, 0.006503)13.343, 55.603, -20.7086
3given(0.999782, -0.018786, 0.009149), (-0.008709, 0.023367, 0.999689), (-0.018994, -0.99955, 0.023198)-11.2435, 20.0008, 55.7471
4given(0.999223, -0.006459, 0.03887), (-0.038098, 0.093375, 0.994902), (-0.010055, -0.99561, 0.093057)-12.1863, 17.2248, 54.3182
5given(0.998796, -0.035591, 0.033755), (-0.036358, -0.999088, 0.022386), (0.032927, -0.023586, -0.999179)-22.789, 76.9722, 35.5722
6given(0.999078, -0.033958, 0.026286), (-0.035198, -0.998215, 0.048245), (0.0246, -0.049125, -0.99849)-22.7921, 76.3346, 36.7642

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Components

#1: Protein
ABL TYROSINE KINASE


Mass: 6423.080 Da / Num. of mol.: 4 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00519
#2: Protein/peptide
PEPTIDE P41


Mass: 1035.149 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growMethod: vapor diffusion / pH: 3.1
Details: CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM ...Details: CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM CHLORIDE, AND 1MM DTT/EDTA. THE HANGING DROP CONTAINED 1:1 RATIO OF RESERVOIR AND PROTEIN-PEPTIDE SOLUTIONS., vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Mcitric acid1reservoir
22 Mammonium sulfate1reservoir
30.2 M1reservoirNaCl
41 mMdithiothreitol1reservoir
51 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.6→39.3 Å / Num. obs: 226846 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.59 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.58 / % possible all: 98.4
Reflection
*PLUS
Num. obs: 34430 / Num. measured all: 226846

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABO
Resolution: 1.65→8 Å / Cross valid method: FREE R-FACTOR / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.266 -10 %RANDOM
Rwork0.205 ---
Obs0.205 31081 --
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 20 269 2415
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.678
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
Xplor file
Refinement-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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