[English] 日本語
Yorodumi
- PDB-1abo: CRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 D... -

+
Open data


ID or keywords:

Loading...

-
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 / Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / negative regulation of small GTPase mediated signal transduction / exocyst / RHO GTPases Activate WASPs and WAVEs / semaphorin receptor binding / Cyclin D associated events in G1 / RAC1 GTPase cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...regulation of actin filament depolymerization / Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / negative regulation of small GTPase mediated signal transduction / exocyst / RHO GTPases Activate WASPs and WAVEs / semaphorin receptor binding / Cyclin D associated events in G1 / RAC1 GTPase cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DN4 thymocyte differentiation / regulation of cellular senescence / response to epinephrine / RUNX1 regulates transcription of genes involved in differentiation of HSCs / podocyte apoptotic process / transitional one stage B cell differentiation / regulation of modification of synaptic structure / Regulation of actin dynamics for phagocytic cup formation / regulation of Rac protein signal transduction / delta-catenin binding / DNA conformation change / ruffle assembly / microspike assembly / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / cerebellum morphogenesis / regulation of extracellular matrix organization / positive regulation of blood vessel branching / circulatory system development / 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 / establishment of epithelial cell apical/basal polarity / activated T cell proliferation / regulation of Cdc42 protein signal transduction / proline-rich region binding / mitogen-activated protein kinase binding / positive regulation of dendrite development / syntaxin binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of T cell differentiation / cardiac muscle cell proliferation / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / phagocytosis, engulfment / negative regulation of cell-cell adhesion / B cell proliferation / cell leading edge / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / semaphorin-plexin signaling pathway / neuromuscular process controlling balance / phagocytic cup / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / negative regulation of BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / endothelial cell migration / bicellular tight junction / signal transduction in response to DNA damage / positive regulation of T cell migration / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / canonical NF-kappaB signal transduction / phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / spleen development / cellular response to transforming growth factor beta stimulus / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / ruffle / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / response to endoplasmic reticulum stress / ephrin receptor binding / positive regulation of interleukin-2 production / actin filament polymerization / ERK1 and ERK2 cascade / post-embryonic development / GTPase activator activity / SH2 domain binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / positive regulation of GTPase activity
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 ...: / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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