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- PDB-5a0f: Crystal structure of Yersinia Afp18-modified RhoA -

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Basic information

Entry
Database: PDB / ID: 5a0f
TitleCrystal structure of Yersinia Afp18-modified RhoA
ComponentsTRANSFORMING PROTEIN RHOA
KeywordsSIGNALING PROTEIN / N-ACETYLGLUCOSAMINE-PROTEIN / TYROSINE GLYCOSYLATION / GTPASE / BACTERIAL TOXIN EFFECTOR / TYPE 6 SECRETION SYSTEM / ANTIFEEDING PROPHAGE
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / apical junction assembly / regulation of modification of postsynaptic structure / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / negative regulation of cell size / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / Wnt signaling pathway, planar cell polarity pathway / odontogenesis / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / EPHA-mediated growth cone collapse / myosin binding / stress fiber assembly / positive regulation of cytokinesis / regulation of neuron projection development / RHOC GTPase cycle / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / ficolin-1-rich granule membrane / RHOA GTPase cycle / mitotic spindle assembly / negative regulation of cell-substrate adhesion / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / positive regulation of T cell migration / endothelial cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / GPVI-mediated activation cascade / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / cell periphery / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of actin cytoskeleton organization / kidney development / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell morphogenesis / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / neuron migration / G beta:gamma signalling through PI3Kgamma / Ovarian tumor domain proteases / cell junction
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Transforming protein RhoA
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJank, T. / Schimpl, M. / van Aalten, D.M.
CitationJournal: Nat Commun / Year: 2015
Title: Tyrosine glycosylation of Rho by Yersinia toxin impairs blastomere cell behaviour in zebrafish embryos.
Authors: Jank, T. / Eckerle, S. / Steinemann, M. / Trillhaase, C. / Schimpl, M. / Wiese, S. / van Aalten, D.M. / Driever, W. / Aktories, K.
History
DepositionApr 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2017Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author / entity_src_gen
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSFORMING PROTEIN RHOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2284
Polymers20,4671
Non-polymers7603
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.392, 91.392, 56.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TRANSFORMING PROTEIN RHOA / RAS-LIKE GTP-BINDING PROTEIN RHO / RHO CDNA CLONE 12 / H12


Mass: 20467.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-181
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATION AT Y 34 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61586
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): N-ACETYL-D-GLUCOSAMINE IS COVALENTLY ATTACHED TO THE HYDROXYL GROUP ...N-ACETYL-D-GLUCOSAMINE (NAG): N-ACETYL-D-GLUCOSAMINE IS COVALENTLY ATTACHED TO THE HYDROXYL GROUP OF TYROSINE 34 IN THE ALPHA CONFIGURATION.

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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: 2.93 Å3/Da / Density % sol: 58.07 % / Description: NONE
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SODIUM ACETATE, PH 5 AND 1.5 M AMMONIUM SULFATE; SITTING-DROP VAPOR-DIFFUSION AT 293.15 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU CCD / Detector: CCD / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31941 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPF

1dpf


Resolution: 2→91.39 Å / SU B: 2.912 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21292 866 5.2 %RANDOM
Rwork0.20533 ---
obs0.20571 15937 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.808 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2→91.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 47 80 1526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191476
X-RAY DIFFRACTIONr_bond_other_d0.0010.021391
X-RAY DIFFRACTIONr_angle_refined_deg1.6712.0152007
X-RAY DIFFRACTIONr_angle_other_deg2.36633214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10524.76965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84615254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.436159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211617
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02306
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2371.788711
X-RAY DIFFRACTIONr_mcbond_other1.2361.788710
X-RAY DIFFRACTIONr_mcangle_it1.9012.673887
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1092.117764
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 62 -
Rwork0.21 1133 -
obs--98.52 %

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