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- PDB-9qcd: Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in comp... -

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Basic information

Entry
Database: PDB / ID: 9qcd
TitleMicro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide
Components
  • GRB2-associated-binding protein 1
  • Tyrosine-protein phosphatase non-receptor type 11
KeywordsSIGNALING PROTEIN / SH2-domain / phosphatase / PTPN11 / phospho-tyrosine
Function / homology
Function and homology information


negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / endothelial cell chemotaxis / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / endothelial cell chemotaxis / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / cerebellar cortex formation / negative regulation of neutrophil activation / Activated NTRK2 signals through PI3K / positive regulation of hormone secretion / MET receptor recycling / regulation of protein export from nucleus / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / Signaling by Leptin / positive regulation of ossification / MET activates PTPN11 / hormone metabolic process / MET activates RAP1 and RAC1 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / ERBB signaling pathway / face morphogenesis / platelet formation / vascular endothelial growth factor signaling pathway / triglyceride metabolic process / organ growth / megakaryocyte development / Interleukin-20 family signaling / negative regulation of type I interferon production / Interleukin-6 signaling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / peptide hormone receptor binding / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / Bergmann glial cell differentiation / inner ear development / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / phosphoprotein phosphatase activity / Regulation of IFNA/IFNB signaling / positive regulation of intracellular signal transduction / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / PI3K events in ERBB2 signaling / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / positive regulation of insulin receptor signaling pathway / GAB1 signalosome / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / Regulation of IFNG signaling / Activated NTRK2 signals through FRS2 and FRS3 / Signaling by FGFR4 in disease / GPVI-mediated activation cascade / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / negative regulation of T cell proliferation / cell adhesion molecule binding / Signaling by FLT3 ITD and TKD mutants / T cell costimulation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / hormone-mediated signaling pathway / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / phosphotyrosine residue binding / protein-tyrosine-phosphatase / FLT3 Signaling / Signaling by FGFR1 in disease / signaling adaptor activity / Downstream signal transduction / positive regulation of mitotic cell cycle / homeostasis of number of cells within a tissue / axonogenesis / protein tyrosine phosphatase activity
Similarity search - Function
GRB2-associated-binding protein 1-4-like / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / PH domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...GRB2-associated-binding protein 1-4-like / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / PH domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11 / GRB2-associated-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.2 Å
AuthorsMachner, L. / Shaikhqasem, A. / Hamdi, F. / Breithaupt, C. / Parthier, C. / Kyrilis, F.L. / Kastritis, P.L. / Feller, S.M. / Stubbs, M.T.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Regional Development FundEuropean Union
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2026
Title: Strategies for mitigating radiation damage and improving data completeness in 3D electron diffraction of protein crystals
Authors: Shaikhqasem, A. / Hamdi, F. / Machner, L. / Parthier, C. / Breithaupt, C. / Kyrilis, F.L. / Feller, S.M. / Kastritis, P.L. / Stubbs, M.T.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Tyrosine-protein phosphatase non-receptor type 11
C: GRB2-associated-binding protein 1


Theoretical massNumber of molelcules
Total (without water)32,8412
Polymers32,8412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-23 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.595, 82.253, 117.764
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

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 11 / Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP- ...Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP-2 / Shp2 / SH-PTP3


Mass: 25133.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein GRB2-associated-binding protein 1 / GRB2-associated binder 1 / Growth factor receptor bound protein 2-associated protein 1


Mass: 7707.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13480
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Image recordingElectron dose: 0.05 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
EM diffraction shellResolution: 3.2→33.7 Å / Fourier space coverage: 88.8 % / Multiplicity: 11.9 / Num. of structure factors: 4729 / Phase residual: 0.1 °
EM diffraction statsDetails: Data Collection Statistics: number of reflections: 56190 (last shell:9163) number of unique reflections: 4729 (last shell:744) R-meas: 0.802 (last shell: 2.20) CC 1/2: 0.94 (last shell: 0.53) ...Details: Data Collection Statistics: number of reflections: 56190 (last shell:9163) number of unique reflections: 4729 (last shell:744) R-meas: 0.802 (last shell: 2.20) CC 1/2: 0.94 (last shell: 0.53) : 3.29 (last shell: 1.41) Completeness: 88.8% (last shell: 89.7%) Multiplicity: 11.9 (last shell:12.3)
Fourier space coverage: 88.8 % / High resolution: 3.2 Å / Num. of intensities measured: 56190 / Num. of structure factors: 4729 / Phase error rejection criteria: 0 / Rmerge: 0.8
ReflectionResolution: 3.2→33.7 Å / Num. obs: 4729 / % possible obs: 88.8 % / Redundancy: 11.9 % / Biso Wilson estimate: 62.54 Å2 / CC1/2: 0.94 / Rrim(I) all: 0.802 / Net I/σ(I): 3.29 / Num. measured all: 56190
Reflection shellResolution: 3.2→4.03 Å / % possible obs: 89.7 % / Redundancy: 12.3 % / Mean I/σ(I) obs: 1.41 / Num. measured obs: 9163 / Num. unique obs: 744 / CC1/2: 0.53 / Rrim(I) all: 2.2

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
Image processingDetails: ELECTRON CRYSTALLOGRAPHY
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 30.59 Å / B: 82.25 Å / C: 117.76 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: OTHER / Symmetry type: 3D CRYSTAL
RefinementResolution: 3.2→33.72 Å / SU ML: 0.4085 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Crystallographic refinement was performed using - a riding hydrogen model - electron scattering factors in PHENIX (version 1.20.1_4487)
RfactorNum. reflection% reflection
Rfree0.3527 238 5.04 %
Rwork0.3005 4487 -
obs0.3032 4725 88.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0031968
ELECTRON CRYSTALLOGRAPHYf_angle_d0.64772658
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0411293
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0053341
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d15.0428746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-4.030.36231220.33522194ELECTRON CRYSTALLOGRAPHY89.59
4.03-33.720.3471160.28122293ELECTRON CRYSTALLOGRAPHY88.18

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