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- PDB-1gzs: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE GEF DOMAIN OF THE SA... -

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Basic information

Entry
Database: PDB / ID: 1gzs
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE GEF DOMAIN OF THE SALMONELLA TYPHIMURIUM SOPE TOXIN AND HUMAN Cdc42
Components
  • GTP-BINDING PROTEIN
  • SOPE
KeywordsTOXIN/CELL CYCLE / COMPLEX (TOXIN-CELL CYCLE PROTEIN) / SOPE / CDC42 / SALMONELLA TYPHIMURIUM / GEF / TOXIN / GTP- BINDING / LIPOPROTEIN / PRENYLATION / TOXIN-CELL CYCLE complex
Function / homology
Function and homology information


GPVI-mediated activation cascade / EGFR downregulation / : / Regulation of actin dynamics for phagocytic cup formation / CD28 dependent Vav1 pathway / EPHB-mediated forward signaling / DCC mediated attractive signaling / VEGFA-VEGFR2 Pathway / Myogenesis / RHO GTPases activate KTN1 ...GPVI-mediated activation cascade / EGFR downregulation / : / Regulation of actin dynamics for phagocytic cup formation / CD28 dependent Vav1 pathway / EPHB-mediated forward signaling / DCC mediated attractive signaling / VEGFA-VEGFR2 Pathway / Myogenesis / RHO GTPases activate KTN1 / RHO GTPases activate IQGAPs / RHO GTPases activate PAKs / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / G beta:gamma signalling through CDC42 / : / Factors involved in megakaryocyte development and platelet production / modification of synaptic structure / Cdc42 protein signal transduction / GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / cell projection assembly / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of lamellipodium assembly / regulation of stress fiber assembly / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / microtubule organizing center / lamellipodium membrane / RHOU GTPase cycle / macrophage differentiation / CDC42 GTPase cycle / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity
Similarity search - Function
Guanine nucleotide exchange factor SopE, N-terminal domain / Salmonella type III secretion SopE effector N-terminus / SopE-like, GEF domain / Guanine nucleotide exchange factor SopE / Guanine nucleotide exchange factor SopE, GEF domain / SopE-like, GEF domain superfamily / SopE GEF domain / SopE-like GEF fold / Cdc42 / Small GTPase Rho ...Guanine nucleotide exchange factor SopE, N-terminal domain / Salmonella type III secretion SopE effector N-terminus / SopE-like, GEF domain / Guanine nucleotide exchange factor SopE / Guanine nucleotide exchange factor SopE, GEF domain / SopE-like, GEF domain superfamily / SopE GEF domain / SopE-like GEF fold / Cdc42 / Small GTPase Rho / Small GTPase Rho domain profile. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Guanine nucleotide exchange factor SopE / Cell division control protein 42 homolog / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsBuchwald, G. / Friebel, A. / Galan, J.E. / Hardt, W.D. / Wittinghofer, A. / Scheffzek, K.
CitationJournal: Embo J. / Year: 2002
Title: Structural Basis for the Reversible Activation of a Rho Protein by the Bacterial Toxin Sope
Authors: Buchwald, G. / Friebel, A. / Galan, J.E. / Hardt, W.D. / Wittinghofer, A. / Scheffzek, K.
History
DepositionJun 5, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-BINDING PROTEIN
B: SOPE
C: GTP-BINDING PROTEIN
D: SOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53310
Polymers75,9574
Non-polymers5766
Water2,882160
1
A: GTP-BINDING PROTEIN
B: SOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3636
Polymers37,9782
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: GTP-BINDING PROTEIN
D: SOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1714
Polymers37,9782
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.545, 87.545, 200.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.36758, -0.26308, 0.892), (0.16837, -0.92448, -0.34204), (0.91462, 0.27591, -0.29552)
Vector: -96.45638, 136.63788, 56.7105)

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Components

#1: Protein GTP-BINDING PROTEIN / PLACENTAL ISOFORM / CDC42 G25K


Mass: 19918.832 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25763, UniProt: P60953*PLUS
#2: Protein SOPE


Mass: 18059.607 Da / Num. of mol.: 2
Fragment: GUANINE NUCTLEOTIDE EXCHANGE FACTOR (GEF-DOMAIN), RESIDUES 78-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O52623
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 58 %
Crystal growpH: 5.6
Details: 1.9 M (NH4)2SO4, 0.1 M SODIUM CITRATE PH 5.6, 2% PEG400, 0.05 M BETAINE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
144 mg/mlprotein1drop
21.9 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoirpH5.6
42 %PEG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 40507 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.112 / Net I/σ(I): 15.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.328 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.112
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 4737 / Rmerge(I) obs: 0.328

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→19.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5242854.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4012 10 %RANDOM
Rwork0.226 ---
obs0.226 40297 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1614 Å2 / ksol: 0.381516 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å22.1 Å20 Å2
2---1.34 Å20 Å2
3---2.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 30 160 5498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 659 10 %
Rwork0.23 5943 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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