[English] 日本語
Yorodumi
- PDB-3uf4: Crystal structure of a SH3 and SH2 domains of FYN protein (Proto-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uf4
TitleCrystal structure of a SH3 and SH2 domains of FYN protein (Proto-concogene Tyrosine-protein kinase Fyn) from Mus musculus at 1.98 A resolution
ComponentsTyrosine-protein kinase Fyn, Isoform 2
KeywordsTRANSFERASE / Phosphorylation / Host-virus interaction / Protein-Tyrosine Kinases / src Homology Domains / src-Family Kinases / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


NTRK2 activates RAC1 / : / Nephrin family interactions / Platelet Adhesion to exposed collagen / Dectin-2 family / DCC mediated attractive signaling / Reelin signalling pathway / CD28 dependent PI3K/Akt signaling / PECAM1 interactions / CD28 dependent Vav1 pathway ...NTRK2 activates RAC1 / : / Nephrin family interactions / Platelet Adhesion to exposed collagen / Dectin-2 family / DCC mediated attractive signaling / Reelin signalling pathway / CD28 dependent PI3K/Akt signaling / PECAM1 interactions / CD28 dependent Vav1 pathway / Ephrin signaling / Signaling by ERBB2 / CD28 co-stimulation / NCAM signaling for neurite out-growth / CTLA4 inhibitory signaling / Regulation of KIT signaling / : / EPHA-mediated growth cone collapse / CRMPs in Sema3A signaling / GPVI-mediated activation cascade / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / : / EPHB-mediated forward signaling / Signaling by SCF-KIT / FCGR activation / response to singlet oxygen / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / negative regulation of hydrogen peroxide biosynthetic process / RAF/MAP kinase cascade / response to xenobiotic stimulus => GO:0009410 / Cell surface interactions at the vascular wall / perinuclear endoplasmic reticulum / PIP3 activates AKT signaling / Regulation of signaling by CBL / growth factor receptor binding / heart process / cellular response to L-glutamate / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / CD209 (DC-SIGN) signaling / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / activated T cell proliferation / positive regulation of cysteine-type endopeptidase activity / VEGFA-VEGFR2 Pathway / CD4 receptor binding / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / dendrite morphogenesis / cellular response to peptide hormone stimulus / DAP12 signaling / peptide hormone receptor binding / CD8 receptor binding / cellular response to platelet-derived growth factor stimulus / glial cell projection / response to amyloid-beta / cellular response to glycine / alpha-tubulin binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of protein targeting to membrane / postsynaptic density, intracellular component / detection of mechanical stimulus involved in sensory perception of pain / phosphatidylinositol 3-kinase binding / T cell receptor binding / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / forebrain development / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / cell surface receptor protein tyrosine kinase signaling pathway / myelination / tubulin binding / ephrin receptor binding / G protein-coupled receptor binding / cell periphery / actin filament / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / tau protein binding / response to hydrogen peroxide / negative regulation of protein catabolic process / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / disordered domain specific binding / T cell receptor signaling pathway / regulation of cell population proliferation / regulation of cell shape / cell body / protein tyrosine kinase activity / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / adaptive immune response / negative regulation of neuron apoptotic process
Similarity search - Function
Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain ...Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a SH3 and SH2 domains of FYN protein (Proto-concogene Tyrosine-protein kinase Fyn) from Mus musculus at 1.98 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_asym_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_ref_seq_dif.details / _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: Tyrosine-protein kinase Fyn, Isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1606
Polymers18,8821
Non-polymers2785
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.220, 35.960, 43.960
Angle α, β, γ (deg.)90.000, 93.560, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Tyrosine-protein kinase Fyn, Isoform 2 / Proto-oncogene c-Fyn / p59-Fyn


Mass: 18881.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BC092217, Fyn / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: P39688, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 82-244) WAS EXPRESSED WITH AN N-TERMINAL EXPRESSION / PURIFICATION TAG ...THE CONSTRUCT (RESIDUES 82-244) WAS EXPRESSED WITH AN N-TERMINAL EXPRESSION / PURIFICATION TAG MGSDKIHHHHHHAEIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVA PTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERV KGIAFMEFIRPIPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYR EPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAK SLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTLEISGEPTTHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. WHILE THE CLONED SEQUENCE MATCHES ISOFORM 2 (ALSO KNOWN AS T) FOR UNIPROTKB ID P39688, RESIDUE NUMBERING IS BASED ON THE UNIPROT "CANONICAL" ISOFORM 1 (ALSO KNOWN AS B).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4.3M NaCl, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.98→43.876 Å / Num. obs: 14960 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.893 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.98-2.050.8111.86306142096.9
2.05-2.130.5353.16356141195.1
2.13-2.230.4023.87506154598.9
2.23-2.350.325.26548143993.4
2.35-2.490.20877045143599.9
2.49-2.690.14410.17381155198
2.69-2.960.08116.17421152199.7
2.96-3.380.04227.27152149599.6
3.38-4.250.03337.16611147796.9
4.250.02842.57413161699.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
MOLREPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→43.876 Å / Cor.coef. Fo:Fc: 0.9501 / Cor.coef. Fo:Fc free: 0.9344 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. HOWEVER, THE SE-MET SIDE-CHAIN IS DISORDERED. 2. ATOM RECORD CONTAINS SUM OF TLS AND ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. HOWEVER, THE SE-MET SIDE-CHAIN IS DISORDERED. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. GLYCEROL, SODIUM AND CHLORIDE MODELED IS PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 749 5.02 %RANDOM
Rwork0.1995 ---
obs0.2007 14932 97.59 %-
Displacement parametersBiso max: 135.7 Å2 / Biso mean: 47.7247 Å2 / Biso min: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.7981 Å20 Å2-0.2091 Å2
2---2.2132 Å20 Å2
3----0.5849 Å2
Refine analyzeLuzzati coordinate error obs: 0.327 Å
Refinement stepCycle: LAST / Resolution: 1.98→43.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 15 87 1400
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d642SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes205HARMONIC5
X-RAY DIFFRACTIONt_it1375HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion173SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1519SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1375HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1867HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion2.17
LS refinement shellResolution: 1.98→2.12 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2649 139 5.39 %
Rwork0.2679 2441 -
all0.2678 2580 -
obs--97.59 %
Refinement TLS params.Method: refined / Origin x: 21.1161 Å / Origin y: 0.6251 Å / Origin z: 7.484 Å
111213212223313233
T0.0115 Å20.0194 Å2-0.0412 Å2--0.0937 Å2-0.0282 Å2---0.0416 Å2
L1.6568 °21.3756 °21.755 °2-1.249 °20.9993 °2--2.5932 °2
S0.0598 Å °-0.1308 Å °-0.0258 Å °-0.0067 Å °-0.0633 Å °0.0544 Å °0.0903 Å °-0.3637 Å °0.0035 Å °
Refinement TLS groupSelection details: { A|85 - A|244 }

+
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