[English] 日本語
Yorodumi
- PDB-2fo0: Organization of the SH3-SH2 Unit in Active and Inactive Forms of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fo0
TitleOrganization of the SH3-SH2 Unit in Active and Inactive Forms of the c-Abl Tyrosine Kinase
ComponentsProto-oncogene tyrosine-protein kinase ABL1 (1B ISOFORM)
KeywordsTRANSFERASE / N-terminal cap / autoinhibition / myristoylation / SH3-SH2 clamp / phosphoserine
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 / nicotinate-nucleotide adenylyltransferase activity / positive regulation blood vessel branching ...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 / nicotinate-nucleotide adenylyltransferase activity / positive regulation blood vessel branching / 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 / alpha-beta T cell differentiation / 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 / positive regulation of interferon-gamma production => GO:0032729 / mitogen-activated protein kinase binding / proline-rich region binding / syntaxin binding / DNA damage induced protein phosphorylation / cellular response to dopamine / 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 cell adhesion / regulation of hematopoietic stem cell differentiation / negative regulation of endothelial cell apoptotic process / 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 / positive regulation of stress fiber assembly / four-way junction DNA binding / signal transduction in response to DNA damage / regulation of actin cytoskeleton organization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / regulation of autophagy / cellular protein modification process / spleen development / negative regulation of I-kappaB kinase/NF-kappaB signaling / post-embryonic development / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of mitotic cell cycle / 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 / sequence-specific double-stranded DNA binding / actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / establishment of protein localization / SH3 domain binding / postsynapse / autophagy / 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
Tyrosine-protein kinase, catalytic domain / SH2 domain / Protein kinase domain / SH2 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH3 domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / F-actin binding / Protein kinase, ATP binding site ...Tyrosine-protein kinase, catalytic domain / SH2 domain / Protein kinase domain / SH2 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH3 domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / F-actin binding / Protein kinase, ATP binding site / Tyrosine-protein kinase ABL1/transforming protein Abl / Tyrosine-protein kinase ABL, SH2 domain / Protein tyrosine and serine/threonine kinase / SH3-like domain superfamily / SH2 domain superfamily / SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 type barrels. / Roll / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Tyrosine-protein kinase ABL1 / Tyrosine-protein kinase ABL1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsNagar, B. / Hantschel, O. / Seeliger, M. / Davies, J.M. / Weis, W.I. / Superti-Furga, G. / Kuriyan, J.
CitationJournal: Mol.Cell / Year: 2006
Title: Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase.
Authors: Nagar, B. / Hantschel, O. / Seeliger, M. / Davies, J.M. / Weis, W.I. / Superti-Furga, G. / Kuriyan, J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Remark 999SEQUENCE Residues 15-56 of the original protein sequence were deleted. Myristoyl group (MYR) is ...SEQUENCE Residues 15-56 of the original protein sequence were deleted. Myristoyl group (MYR) is covalently attached to the N-terminus of the protein.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase ABL1 (1B ISOFORM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2925
Polymers56,4521
Non-polymers8404
Water2,612145
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)79.688, 117.266, 60.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Proto-oncogene tyrosine-protein kinase ABL1 (1B ISOFORM)


Mass: 56452.371 Da / Num. of mol.: 1
Fragment: Abl N-cap (residues 1-531, residues 15-56 deleted)
Mutation: D382N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: c-Abl / Plasmid: PFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00519-2, UniProt: P00519*PLUS, EC: 2.7.1.112
#2: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-P16 / 6-(2,6-DICHLOROPHENYL)-2-{[3-(HYDROXYMETHYL)PHENYL]AMINO}-8-METHYLPYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE / PD166326


Mass: 427.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16Cl2N4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.27→48.14 Å / Num. all: 25639 / Num. obs: 25639 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 14.6
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2026 / Rsym value: 0.289 / % possible all: 76.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPK
Resolution: 2.27→48.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 318702.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1656 6.8 %RANDOM
Rwork0.21 ---
Obs0.21 24283 90.3 %-
All-24283 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6955 Å2 / ksol: 0.376791 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--9.32 Å20 Å20 Å2
2---10.46 Å20 Å2
3---19.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.27→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 56 145 3949
Refine LS restraints
Refinement-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 235 7.3 %
Rwork0.27 3000 -
Obs-3235 73.5 %
Xplor file
Refinement-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2ligands.parligands.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more