[English] 日本語
Yorodumi
- PDB-7a2l: Crystal structure of the Fyn SH3 domain mutant E129Q in space gro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a2l
TitleCrystal structure of the Fyn SH3 domain mutant E129Q in space group C21 at pH 4.0
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / heart process / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / heart process / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / reelin-mediated signaling pathway / Platelet Adhesion to exposed collagen / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / FLT3 signaling through SRC family kinases / activated T cell proliferation / positive regulation of protein localization to membrane / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / CD4 receptor binding / negative regulation of dendritic spine maintenance / feeding behavior / cellular response to L-glutamate / Co-stimulation by CD28 / Nephrin family interactions / DCC mediated attractive signaling / natural killer cell activation / EPH-Ephrin signaling / Ephrin signaling / dendritic spine maintenance / CD28 dependent Vav1 pathway / growth factor receptor binding / tau-protein kinase activity / cellular response to peptide hormone stimulus / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / dendrite morphogenesis / peptide hormone receptor binding / CD8 receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / forebrain development / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / glial cell projection / CD28 dependent PI3K/Akt signaling / positive regulation of protein targeting to membrane / Role of LAT2/NTAL/LAB on calcium mobilization / alpha-tubulin binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / postsynaptic density, intracellular component / cellular response to transforming growth factor beta stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / T cell receptor binding / phospholipase binding / phosphatidylinositol 3-kinase binding / GPVI-mediated activation cascade / ephrin receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / Regulation of signaling by CBL / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / peptidyl-tyrosine phosphorylation / Cell surface interactions at the vascular wall / learning / actin filament / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / protein catabolic process / G protein-coupled receptor binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / positive regulation of neuron projection development / modulation of chemical synaptic transmission / Signaling by CSF1 (M-CSF) in myeloid cells / tau protein binding / positive regulation of protein localization to nucleus
Similarity search - Function
: / Fyn/Yrk, 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 ...: / Fyn/Yrk, 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 / 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
FORMIC ACID / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCamara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: To be published
Title: Crystal structure of the Fyn SH3 domain mutant E129Q in space group C21 at pH 4.0
Authors: Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn
B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7045
Polymers13,5892
Non-polymers1153
Water79344
1
A: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9094
Polymers6,7941
Non-polymers1153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Fyn


Theoretical massNumber of molelcules
Total (without water)6,7941
Polymers6,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.584, 45.896, 42.938
Angle α, β, γ (deg.)90.000, 97.120, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 85 through 93 or (resid 94...
21(chain B and ((resid 85 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTYRTYR(chain A and (resid 85 through 93 or (resid 94...AA85 - 933 - 11
12GLUGLUARGARG(chain A and (resid 85 through 93 or (resid 94...AA94 - 9612 - 14
13THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
14THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
15THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
16THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
21THRTHRTHRTHR(chain B and ((resid 85 and (name N or name...BB853
22GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 1411 - 59
23GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 1411 - 59
24GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 1411 - 59
25GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 1411 - 59

-
Components

#1: Protein Tyrosine-protein kinase Fyn / Proto-oncogene Syn / Proto-oncogene c-Fyn / Src-like kinase / SLK / p59-Fyn


Mass: 6794.351 Da / Num. of mol.: 2 / Mutation: E129Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 3.5M sodium formate, 0.1M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→19.48 Å / Num. obs: 21066 / % possible obs: 99.5 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.052 / Rrim(I) all: 0.096 / Net I/σ(I): 7.1
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
1.9-1.943.20.90624217630.6840.6011.0911.399.7
8.91-19.482.90.093171090.9870.0620.1118.291

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA6

3ua6


Resolution: 1.9→19.48 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 36.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1105 5.25 %
Rwork0.207 19961 -
obs0.2098 21066 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.56 Å2 / Biso mean: 52.5814 Å2 / Biso min: 23.78 Å2
Refinement stepCycle: final / Resolution: 1.9→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 10 44 965
Biso mean--64.3 46.56 -
Num. residues----116
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A450X-RAY DIFFRACTION8.734TORSIONAL
12B450X-RAY DIFFRACTION8.734TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.990.38531360.34142430256693
1.99-2.090.3461470.27632458260595
2.09-2.220.32751430.27122481262496
2.22-2.390.32011510.24552449260095
2.39-2.630.31061260.28342526265297
2.63-3.010.33071360.24592530266697
3.01-3.790.24021420.19032536267898
3.79-19.480.19151240.14942551267597
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.84-5.9338-0.04326.61451.45354.697-0.7005-0.5350.03880.49680.64290.2350.36330.16430.1650.23760.03680.01240.37350.00180.174721.79221.64913.4656
26.75020.6773-0.75593.96193.77173.8857-0.3485-0.2806-0.70830.23870.31350.19720.18280.3389-0.03170.34750.04130.07840.41980.01360.371423.5764-7.59647.2315
32.0881-0.96061.46418.44770.0162.2958-0.4490.23770.0336-0.47610.4751-0.6842-0.1920.69920.06210.3009-0.0081-0.01150.7171-0.13680.389829.73512.454910.0047
44.8451-4.45975.08218.4784-5.56765.3736-0.470.3791-0.2667-0.21150.3386-1.04390.31931.07820.01410.3216-0.00950.04560.5905-0.07560.396530.1935-0.33178.4699
57.5727-5.3137-2.95843.73552.42776.93390.7222-0.1579-1.22840.83710.7215-0.81712.19930.7331-1.25840.59450.155-0.0850.447-0.02120.596130.0712-6.197717.9752
68.8481-2.09220.78438.45773.39228.7319-0.17360.0503-0.21410.17120.2729-0.41510.04710.5198-0.09980.19670.0447-0.00870.37020.02570.238225.29472.71649.5055
75.94631.7518-0.66115.5583-1.77897.0855-0.127-0.7430.0762-0.0289-0.09030.42210.1187-0.0180.23760.27520.12890.01610.3626-0.00760.33939.710613.540413.434
87.9172-4.7686-2.78696.91171.64639.6142-0.03290.33280.2451-0.3594-0.2948-0.0608-1.0142-0.73450.43080.3390.0206-0.00610.3764-0.01160.299910.26518.48588.8564
99.6032-0.715-0.15456.97646.61516.9722-0.076-0.40650.1692-0.0238-0.16780.0853-0.0965-0.62610.2070.33040.07870.0250.37010.07240.201911.026715.38211.2338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 94 )A85 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 104 )A95 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 118 )A105 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 124 )A119 - 124
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 129 )A125 - 129
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 141 )A130 - 141
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 104 )B83 - 104
8X-RAY DIFFRACTION8chain 'B' and (resid 105 through 123 )B105 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 141 )B124 - 141

+
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