[English] 日本語
Yorodumi
- PDB-2hdx: Crystal structure of the Src homology-2 domain of SH2-B in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hdx
TitleCrystal structure of the Src homology-2 domain of SH2-B in complex with Jak2 pTyr813 phosphopeptide
Components
  • Jak2 protein
  • SH2-B PH domain containing signaling mediator 1 gamma isoform
KeywordsSIGNALING PROTEIN / SH2 / Jak2 / phosphotyrosine / adapter protein
Function / homology
Function and homology information


response to granulocyte macrophage colony-stimulating factor / IFNG signaling activates MAPKs / positive regulation of cell activation / defense response to symbiont / Regulation of IFNG signaling / Growth hormone receptor signaling / Signaling by Erythropoietin / Interleukin-4 and Interleukin-13 signaling / Prolactin receptor signaling / Interleukin-20 family signaling ...response to granulocyte macrophage colony-stimulating factor / IFNG signaling activates MAPKs / positive regulation of cell activation / defense response to symbiont / Regulation of IFNG signaling / Growth hormone receptor signaling / Signaling by Erythropoietin / Interleukin-4 and Interleukin-13 signaling / Prolactin receptor signaling / Interleukin-20 family signaling / Interferon gamma signaling / Interleukin-12 signaling / Signaling by CSF3 (G-CSF) / IL-6-type cytokine receptor ligand interactions / Erythropoietin activates RAS / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-23 signaling / Interleukin-27 signaling / regulation of DNA biosynthetic process / Interleukin-6 signaling / Interleukin-35 Signalling / Inactivation of CSF3 (G-CSF) signaling / Signaling by SCF-KIT / Cyclin D associated events in G1 / RAF activation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / RAF/MAP kinase cascade / Factors involved in megakaryocyte development and platelet production / nuclear receptor-mediated mineralocorticoid signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of growth hormone receptor signaling pathway / interleukin-12 receptor complex / histone H3Y41 kinase activity / interleukin-23 receptor complex / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / thrombopoietin-mediated signaling pathway / collagen-activated signaling pathway / interleukin-12 receptor binding / interleukin-5-mediated signaling pathway / interleukin-23-mediated signaling pathway / activation of Janus kinase activity / response to interleukin-12 / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / myeloid cell differentiation / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / post-embryonic hemopoiesis / erythropoietin-mediated signaling pathway / positive regulation of MHC class II biosynthetic process / acetylcholine receptor binding / positive regulation of natural killer cell proliferation / positive regulation of platelet activation / growth hormone receptor binding / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / positive regulation of platelet aggregation / positive regulation of epithelial cell apoptotic process / positive regulation of cell-substrate adhesion / extrinsic component of cytoplasmic side of plasma membrane / axon regeneration / lamellipodium assembly / response to hydroperoxide / growth hormone receptor signaling pathway / negative regulation of cardiac muscle cell apoptotic process / positive regulation of tyrosine phosphorylation of STAT protein / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of cell-cell adhesion / peptide hormone receptor binding / enzyme-linked receptor protein signaling pathway / positive regulation of interleukin-17 production / response to amine / signaling receptor activator activity / platelet-derived growth factor receptor signaling pathway / insulin receptor substrate binding / response to tumor necrosis factor / positive regulation of SMAD protein signal transduction / growth hormone receptor signaling pathway via JAK-STAT / cell surface receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / phosphatidylinositol 3-kinase binding / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / extrinsic apoptotic signaling pathway / ruffle / hormone-mediated signaling pathway / signaling adaptor activity / negative regulation of cytokine production involved in inflammatory response / endomembrane system / positive regulation of mitotic nuclear division / post-translational protein modification / cellular response to dexamethasone stimulus
Similarity search - Function
SH2B1, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe ...SH2B1, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / : / SH2 domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / SH2 domain / SHC Adaptor Protein / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / PH-like domain superfamily / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase JAK2 / Tyrosine-protein kinase JAK2 / SH2B adapter protein 1 / SH2B adapter protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHu, J. / Hubbard, S.R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for Phosphotyrosine Recognition by the Src Homology-2 Domains of the Adapter Proteins SH2-B and APS.
Authors: Hu, J. / Hubbard, S.R.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH2-B PH domain containing signaling mediator 1 gamma isoform
B: SH2-B PH domain containing signaling mediator 1 gamma isoform
C: SH2-B PH domain containing signaling mediator 1 gamma isoform
D: SH2-B PH domain containing signaling mediator 1 gamma isoform
E: SH2-B PH domain containing signaling mediator 1 gamma isoform
F: SH2-B PH domain containing signaling mediator 1 gamma isoform
G: Jak2 protein
H: Jak2 protein
I: Jak2 protein
J: Jak2 protein
K: Jak2 protein
L: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)81,99212
Polymers81,99212
Non-polymers00
Water5,765320
1
A: SH2-B PH domain containing signaling mediator 1 gamma isoform
G: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-7 kcal/mol
Surface area6470 Å2
MethodPISA
2
B: SH2-B PH domain containing signaling mediator 1 gamma isoform
H: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area6330 Å2
MethodPISA
3
C: SH2-B PH domain containing signaling mediator 1 gamma isoform
I: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-9 kcal/mol
Surface area6280 Å2
MethodPISA
4
D: SH2-B PH domain containing signaling mediator 1 gamma isoform
J: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-7 kcal/mol
Surface area6290 Å2
MethodPISA
5
E: SH2-B PH domain containing signaling mediator 1 gamma isoform
K: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area6360 Å2
MethodPISA
6
F: SH2-B PH domain containing signaling mediator 1 gamma isoform
L: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-7 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.21, 74.19, 239.22
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsSix biological units pack in 12 5 screw axis

-
Components

#1: Protein
SH2-B PH domain containing signaling mediator 1 gamma isoform


Mass: 12275.992 Da / Num. of mol.: 6 / Fragment: SH2 (Residues: 499-607) / Mutation: E583A, E584A, W593H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sh2bpsm1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WVM5, UniProt: Q91ZM2*PLUS
#2: Protein/peptide
Jak2 protein


Mass: 1389.312 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Sequence occurs naturally in Mus musculus (mouse). / References: UniProt: Q7TQD0, UniProt: Q62120*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growpH: 5.6
Details: 25% PEG 4000, 0.1 M sodium citrate, 0.3 M ammonium acetate., pH 5.6

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 33327 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 10.2 / Rsym value: 0.103 / % possible all: 97.6

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2HDV

2hdv


Resolution: 2.35→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 1604 Random
Rwork0.21 --
all0.24 33858 -
obs0.24 32298 -
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5373 0 0 320 5693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d0.7

+
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