[English] 日本語
Yorodumi
- PDB-6f3f: Autoinhibited Src kinase bound to ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f3f
TitleAutoinhibited Src kinase bound to ADP
ComponentsTyrosine-protein kinase
KeywordsSIGNALING PROTEIN / kinase / ADP / autoinhibited
Function / homology
Function and homology information


Activated NTRK3 signals through PI3K / Regulation of gap junction activity / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / angiotensin-activated signaling pathway involved in heart process / Nuclear signaling by ERBB4 / Signaling by EGFR / VEGFR2 mediated cell proliferation / : / DCC mediated attractive signaling ...Activated NTRK3 signals through PI3K / Regulation of gap junction activity / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / angiotensin-activated signaling pathway involved in heart process / Nuclear signaling by ERBB4 / Signaling by EGFR / VEGFR2 mediated cell proliferation / : / DCC mediated attractive signaling / PECAM1 interactions / Ephrin signaling / Signaling by ERBB2 / MET activates PTK2 signaling / CD28 co-stimulation / CTLA4 inhibitory signaling / Regulation of KIT signaling / GAB1 signalosome / EPHA-mediated growth cone collapse / Downregulation of ERBB4 signaling / Downstream signal transduction / EPH-ephrin mediated repulsion of cells / regulation of postsynaptic neurotransmitter receptor activity / Spry regulation of FGF signaling / EPHB-mediated forward signaling / Signaling by SCF-KIT / RAF activation / Regulation of RUNX3 expression and activity / Thrombin signalling through proteinase activated receptors (PARs) / FCGR activation / GRB2:SOS provides linkage to MAPK signaling for Integrins / Cyclin D associated events in G1 / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / Extra-nuclear estrogen signaling / : / regulation of cell projection assembly / Recycling pathway of L1 / regulation of cell-cell adhesion / response to xenobiotic stimulus => GO:0009410 / CLEC7A (Dectin-1) signaling / response to mineralocorticoid / positive regulation of dephosphorylation / PIP3 activates AKT signaling / RHO GTPases Activate Formins / G alpha (i) signalling events / regulation of epithelial cell migration / positive regulation of protein transport / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / growth factor receptor binding / negative regulation of focal adhesion assembly / positive regulation of protein processing / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ADP signalling through P2Y purinoceptor 1 / regulation of protein binding / RET signaling / : / intestinal epithelial cell development / regulation of intracellular estrogen receptor signaling pathway / positive regulation of glucose metabolic process / transcytosis / connexin binding / cellular response to fluid shear stress / VEGFA-VEGFR2 Pathway / response to acidic pH / focal adhesion assembly / positive regulation of small GTPase mediated signal transduction / podosome / positive regulation of podosome assembly / branching involved in mammary gland duct morphogenesis / adherens junction organization / odontogenesis / negative regulation of mitochondrial depolarization / positive regulation of intracellular signal transduction / cellular response to peptide hormone stimulus / osteoclast development / cellular response to fatty acid / regulation of early endosome to late endosome transport / postsynaptic specialization, intracellular component / positive regulation of DNA biosynthetic process / oogenesis / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / cellular response to platelet-derived growth factor stimulus / stress fiber assembly / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / progesterone receptor signaling pathway / uterus development / neurotrophin TRK receptor signaling pathway / negative regulation of telomere maintenance via telomerase / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of anoikis
Similarity search - Function
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 ...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. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
ADENOSINE-5'-DIPHOSPHATE / Neuronal proto-oncogene tyrosine-protein kinase Src / Tyrosine-protein kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41795770496 Å
Authorsvon Raussendorf, F. / Leonard, T.A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP28135 Austria
CitationJournal: Sci Rep / Year: 2017
Title: A switch in nucleotide affinity governs activation of the Src and Tec family kinases.
Authors: von Raussendorf, F. / de Ruiter, A. / Leonard, T.A.
History
DepositionNov 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4893
Polymers52,0381
Non-polymers4522
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-15 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.011, 82.974, 105.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Tyrosine-protein kinase


Mass: 52037.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Src / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q3UKD6, UniProt: P05480*PLUS, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM PIPES, pH 6.5 1.2 M sodium tartrate 20 mM DTT 2 mM ADP 5 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.41→65 Å / Num. obs: 17674 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 34.3898947591 Å2 / Net I/σ(I): 6.1
Reflection shellResolution: 2.41→2.51 Å

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2SRC

2src


Resolution: 2.41795770496→52.5255 Å / SU ML: 0.319898435617 / Cross valid method: FREE R-VALUE / σ(F): 1.34358350621 / Phase error: 26.1574771142
RfactorNum. reflection% reflection
Rfree0.267642283351 872 4.96979368517 %
Rwork0.20792467656 --
obs0.210911359312 17546 99.2870076958 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.8213953531 Å2
Refinement stepCycle: LAST / Resolution: 2.41795770496→52.5255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 28 83 3729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002362028588543733
X-RAY DIFFRACTIONf_angle_d0.582911199215065
X-RAY DIFFRACTIONf_chiral_restr0.0396140306002545
X-RAY DIFFRACTIONf_plane_restr0.00203946487862646
X-RAY DIFFRACTIONf_dihedral_angle_d14.20681807542234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.418-2.56940.3522938454521270.3028496381482763X-RAY DIFFRACTION99.72394755
2.5694-2.76780.3540498224181480.2820293452392677X-RAY DIFFRACTION98.1584433634
2.7678-3.04630.3038767366751460.2428462014922766X-RAY DIFFRACTION99.897084048
3.0463-3.48710.2495055815491570.2008966339012746X-RAY DIFFRACTION99.5883361921
3.4871-4.3930.2416982413661420.1706643458422788X-RAY DIFFRACTION99.1875423155
4.393-52.53790.2376402143371520.1822854461922934X-RAY DIFFRACTION99.2282958199
Refinement TLS params.Method: refined / Origin x: 22.2912602708 Å / Origin y: 83.5075020806 Å / Origin z: 119.521164903 Å
111213212223313233
T0.213220336045 Å20.00110651740131 Å2-0.0568881943948 Å2-0.223449865614 Å20.0108353347993 Å2--0.225287880619 Å2
L1.42813867855 °20.129038436207 °2-0.373951217883 °2-0.94482126093 °2-0.243942630502 °2--1.21421885929 °2
S-0.0270908313887 Å °-0.0966256543793 Å °-0.120483612535 Å °-0.0151274879828 Å °0.0132101507147 Å °0.0292046719676 Å °0.152990772501 Å °0.00180994083774 Å °0.0162422916 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 82 through 529)

+
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://pdbjlvh1.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