[English] 日本語
Yorodumi
- PDB-3nhn: Crystal structure of the SRC-family kinase HCK SH3-SH2-linker reg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nhn
TitleCrystal structure of the SRC-family kinase HCK SH3-SH2-linker regulatory region
ComponentsTyrosine-protein kinase HCK
KeywordsTRANSFERASE / Hck / SH3-SH2-linker / Src family kinase / SFK
Function / homology
Function and homology information


leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / transport vesicle / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / caveola / cell projection / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase HCK, SH2 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 ...Tyrosine-protein kinase HCK, SH2 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 HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsAlvarado, J.J. / Betts, L. / Moroco, J.A. / Smithgall, T.E. / Yeh, J.I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal Structure of the Src Family Kinase Hck SH3-SH2 Linker Regulatory Region Supports an SH3-dominant Activation Mechanism.
Authors: Alvarado, J.J. / Betts, L. / Moroco, J.A. / Smithgall, T.E. / Yeh, J.I.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)22,3121
Polymers22,3121
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.714, 60.714, 49.581
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Tyrosine-protein kinase HCK / Hemopoietic cell kinase / p59-HCK/p60-HCK


Mass: 22311.906 Da / Num. of mol.: 1 / Fragment: UNP residues 72-256, Hck-SH3-SH2-Linker fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta 2
References: UniProt: P08631, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% (v/v) polyethylene glycol 3,350, 0.15 M KSCN, 0.05 M NaCl, and 1:100 dilution of Hck-SH3-SH2-linker crystal seeds (grown in 25% v/v polyethylene glycol 3,350, 0.1 M Tris pH 8.5, 0.2 M ...Details: 25% (v/v) polyethylene glycol 3,350, 0.15 M KSCN, 0.05 M NaCl, and 1:100 dilution of Hck-SH3-SH2-linker crystal seeds (grown in 25% v/v polyethylene glycol 3,350, 0.1 M Tris pH 8.5, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 7, 2009
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.478
ReflectionResolution: 2.61→50 Å / Num. obs: 6220 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Χ2: 1.039 / Net I/σ(I): 33.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.61-2.662.30.2782701.18178.9
2.66-2.72.50.3732891.31391.5
2.7-2.7630.2293011.1598.4
2.76-2.8130.2063141.04699.1
2.81-2.873.10.2022861.113100
2.87-2.9430.1943541.04198.9
2.94-3.013.10.1693121.124100
3.01-3.093.20.1213071100
3.09-3.193.40.0972991.34199.7
3.19-3.293.50.0753301.095100
3.29-3.413.70.0723250.937100
3.41-3.543.70.0723141.07599.7
3.54-3.73.70.0582790.665100
3.7-3.93.80.0633510.758100
3.9-4.143.70.0423211.112100
4.14-4.463.80.0432891.23100
4.46-4.913.80.0343321.027100
4.91-5.623.80.0363261.052100
5.62-7.083.80.0383080.987100
7.08-503.80.0393130.87898.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QCF

1qcf


Resolution: 2.61→25.89 Å / Occupancy max: 1 / Occupancy min: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Stereochemistry target values: TWIN_LSQ_F
Details: RESIDUE NUMBERING FOR THE STRUCTURE IS USING THE HUMAN cSRC NUMBERING
RfactorNum. reflection% reflection
Rfree0.1764 302 5.1 %
Rwork0.1194 --
obs0.1198 5920 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.842 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 99.87 Å2 / Biso mean: 43.0302 Å2 / Biso min: 3.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.4321 Å20 Å2-0 Å2
2---1.4321 Å20 Å2
3---0.3747 Å2
Refinement stepCycle: LAST / Resolution: 2.61→25.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 0 35 1349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071343
X-RAY DIFFRACTIONf_angle_d1.0621811
X-RAY DIFFRACTIONf_chiral_restr0.08191
X-RAY DIFFRACTIONf_plane_restr0.004233
X-RAY DIFFRACTIONf_dihedral_angle_d19.888492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6061-3.28190.27061420.17382784292689
3.2819-23.22770.14021380.09552828296691
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)
11.2493-0.5274-0.48560.85411.12471.6548-0.20590.2010.02170.1289-0.18760.22120.2378-0.13770.35380.1373-0.00520.01050.11340.01620.2169-28.006540.1498-10.0072
20.54870.36170.00680.70570.20420.0856-0.03090.106-0.00950.2335-0.02950.10540.26810.14580.0310.5780.18760.12460.4259-0.03420.2598-13.35525.3807-14.9878
30.72740.2007-0.24820.8353-0.33290.9734-0.0996-0.1578-0.08620.0393-0.0951-0.0067-0.2263-0.0767-0.05690.07580.0575-0.03240.0258-0.00410.0187-4.459316.703-7.9364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 83:142)A83 - 142
2X-RAY DIFFRACTION2(chain A and resid 143:147)A143 - 147
3X-RAY DIFFRACTION3(chain A and resid 148:246)A148 - 246

+
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