[English] 日本語
Yorodumi
- PDB-1g4u: CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPA... -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of neutrophil migration / negative regulation of interleukin-23 production / regulation of hydrogen peroxide metabolic process / Activated NTRK2 signals through CDK5 / localization within membrane / negative regulation of fibroblast migration / negative regulation of receptor-mediated endocytosis / mast cell chemotaxis / Rac protein signal transduction ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / regulation of hydrogen peroxide metabolic process / Activated NTRK2 signals through CDK5 / localization within membrane / negative regulation of fibroblast migration / negative regulation of receptor-mediated endocytosis / mast cell chemotaxis / Rac protein signal transduction / ruffle assembly / engulfment of apoptotic cell / Rho GDP-dissociation inhibitor binding / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / RHO GTPases activate CIT / RHO GTPases activate KTN1 / ruffle organization / positive regulation of neutrophil chemotaxis / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / thioesterase binding / regulation of nitric oxide biosynthetic process / regulation of stress fiber assembly / sphingosine-1-phosphate receptor signaling pathway / Wnt signaling pathway, planar cell polarity pathway / motor neuron axon guidance / cell projection assembly / Nef and signal transduction / Sema4D mediated inhibition of cell attachment and migration / regulation of lamellipodium assembly / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Activation of RAC1 / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / lamellipodium assembly / semaphorin-plexin signaling pathway / Activation of RAC1 downstream of NMDARs / CD28 dependent Vav1 pathway / regulation of cell size / NRAGE signals death through JNK / establishment or maintenance of cell polarity / DSCAM interactions / positive regulation of lamellipodium assembly / small GTPase mediated signal transduction / ficolin-1-rich granule membrane / RHO GTPases activate PAKs / positive regulation of insulin secretion involved in cellular response to glucose stimulus / bone resorption / RHO GTPases activate IQGAPs / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of focal adhesion assembly / positive regulation of microtubule polymerization / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate NADPH Oxidases / cell motility / regulation of actin cytoskeleton organization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / neuron migration / actin filament polymerization / G protein activity / small monomeric GTPase / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of DNA replication / regulation of cell migration / RAC1 GTPase cycle / cell-matrix adhesion / GTPase activator activity / substrate adhesion-dependent cell spreading / cell projection / protein-tyrosine-phosphatase / VEGFR2 mediated vascular permeability / secretory granule membrane / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament organization / protein tyrosine phosphatase activity / Signal transduction by L1 / positive regulation of endothelial cell migration / cytoplasmic ribonucleoprotein granule / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / trans-Golgi network / Signaling by SCF-KIT / ruffle membrane / actin cytoskeleton organization / response to wounding / extrinsic component of cytoplasmic side of plasma membrane
Similarity search - Function
SicP binding / Secreted effector protein SptP, N-terminal domain / Virulence factor YopE uncharacterised domain / Virulence factor YopE, GAP domain superfamily / Virulence factor YopE, GAP domain / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / Globular protein, non-globular alpha/beta subunit / small GTPase Rho family profile. / Small GTPase Rho ...SicP binding / Secreted effector protein SptP, N-terminal domain / Virulence factor YopE uncharacterised domain / Virulence factor YopE, GAP domain superfamily / Virulence factor YopE, GAP domain / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / Globular protein, non-globular alpha/beta subunit / small GTPase Rho family profile. / Small GTPase Rho / Protein tyrosine phosphatase superfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, catalytic / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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
Ras-related C3 botulinum toxin substrate 1 / ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
γ
α
β
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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