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- PDB-1g4u: CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPA... -

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Basic information

Entry
Database: PDB / ID: 1g4u
TitleCRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP BOUND TO RAC1
Components
  • PROTEIN TYROSINE PHOSPHATASE SPTP
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsSIGNALING PROTEIN / virulence factor / GAP / tyrosine phosphatase / 4-helix bundle / GTPase
Function / homology
Function and homology information


regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / dephosphorylation / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / GTPase activator activity / cell-matrix adhesion / cell chemotaxis / substrate adhesion-dependent cell spreading / small monomeric GTPase / protein-tyrosine-phosphatase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / protein tyrosine phosphatase activity / actin filament organization / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / VEGFA-VEGFR2 Pathway
Similarity search - Function
Secreted effector protein SptP, N-terminal domain / SicP binding / Secreted effector protein SptP, N-terminal domain superfamily / Virulence factor YopE uncharacterised domain / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / Globular protein, non-globular alpha/beta subunit / Small GTPase Rho ...Secreted effector protein SptP, N-terminal domain / SicP binding / Secreted effector protein SptP, N-terminal domain superfamily / Virulence factor YopE uncharacterised domain / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / Globular protein, non-globular alpha/beta subunit / Small GTPase Rho / small GTPase Rho family profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 1 / Secreted effector protein SptP
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStebbins, C.E. / Galan, J.E.
CitationJournal: Mol.Cell / Year: 2000
Title: Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1.
Authors: Stebbins, C.E. / Galan, J.E.
History
DepositionOct 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 27, 2021Group: 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_atom_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_atom_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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: PROTEIN TYROSINE PHOSPHATASE SPTP
R: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0825
Polymers62,5302
Non-polymers5513
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-24 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.722, 58.260, 60.324
Angle α, β, γ (deg.)70.03, 69.51, 65.03
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 2 molecules SR

#1: Protein PROTEIN TYROSINE PHOSPHATASE SPTP


Mass: 42127.801 Da / Num. of mol.: 1 / Fragment: SPTP RESIDUES 161-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: SPTP / Plasmid: PGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P74873
#2: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1


Mass: 20402.650 Da / Num. of mol.: 1 / Fragment: RAC1 RESIDUES 1-184 / Mutation: F78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: PGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63000

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Non-polymers , 4 types, 337 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.7
Details: 18 %PEG 400, 0.1M MES, 15mM sodium flouride, 0.1mM aluminum chloride, 2mM DTT, 2mM magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
218 %PEG4001reservoir
315 mMsodium fluoride1reservoir
40.1 mM1reservoirAlCl3
52 mMdithiothreitol1reservoir
62 mM1reservoirMgCl2
70.1 MMES1reservoirpH5.7

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 17, 2000 / Details: Yale mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 28370 / Num. obs: 27264 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 15.13 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.7 / % possible all: 94
Reflection
*PLUS
Num. measured all: 177445

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.258 2009 Random 7% CNS
Rwork0.204 --
all0.204 28370 -
obs0.204 26361 -
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 33 334 4555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.3→2.33 Å /
RfactorNum. reflection
Rfree0.36 51
Rwork0.285 -
obs-1003
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Lowest resolution: 2.3 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.285

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