[English] 日本語
Yorodumi
- PDB-7pw2: Crystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pw2
TitleCrystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E mutant
ComponentsNon-specific protein-tyrosine kinase
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


regulation of cellular component organization / GTPase activator activity / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / regulation of apoptotic process / protein serine/threonine kinase activity / signal transduction / ATP binding / cytosol
Similarity search - Function
Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Bcr-Abl oncoprotein oligomerisation domain / PH domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / PH domain profile. ...Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Bcr-Abl oncoprotein oligomerisation domain / PH domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
non-specific protein-tyrosine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
Model detailsChimera construction Abl-c-Src SH3 domain
AuthorsCamara-Artigas, A. / Salinas Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2006-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Understanding domain swapping in the c-Src SH3 domain through hinge-loop mutagenesis.
Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Martinez, J.C. / Camara-Artigas, A.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Sep 10, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-specific protein-tyrosine kinase


Theoretical massNumber of molelcules
Total (without water)6,7211
Polymers6,7211
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.580, 42.580, 30.407
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Non-specific protein-tyrosine kinase


Mass: 6721.397 Da / Num. of mol.: 1 / Mutation: V73E, A74S, S75R, G76T, D77E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCR/ABL fusion / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A9UF07, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.02 % / Mosaicity: 0.09 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M ammonium sulfate, 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.1→17.44 Å / Num. obs: 21193 / % possible obs: 95.3 % / Redundancy: 2 % / Biso Wilson estimate: 17.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.022 / Rrim(I) all: 0.035 / Net I/σ(I): 9.9 / Num. measured all: 43012
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.1-1.1220.455213410830.6830.3850.61.697
6.03-17.442.10.0312401130.9920.0270.04118.980.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG3

3eg3


Resolution: 1.1→17.44 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 34.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1752 5.36 %
Rwork0.183 30963 -
obs0.1841 32715 75.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.6 Å2 / Biso mean: 27.5203 Å2 / Biso min: 14.31 Å2
Refinement stepCycle: final / Resolution: 1.1→17.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 0 51 472
Biso mean---36.89 -
Num. residues----57
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.130.32691520.27852412256476
1.13-1.160.26881350.24952401253675
1.16-1.20.26381190.21942372249176
1.2-1.240.2421500.22952404255476
1.24-1.290.22441230.21882418254177
1.29-1.350.26631290.19342390251976
1.35-1.420.23991410.19752371251275
1.42-1.510.19161410.21972478261978
1.51-1.630.23191680.21072286245474
1.63-1.790.1769880.19552460254876
1.79-2.050.17091230.19292396251975
2.05-2.580.19591550.17892300245574
2.58-17.440.19651280.16152275240372

+
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