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- PDB-2vy9: Molecular architecture of the stressosome, a signal integration a... -

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Basic information

Entry
Database: PDB / ID: 2vy9
TitleMolecular architecture of the stressosome, a signal integration and transduction hub
ComponentsANTI-SIGMA-FACTOR ANTAGONIST
KeywordsGENE REGULATION / MOORELLA THERMOACETICA / RSBS / STRESSOSOME / STAS DOMAIN / BACILLUS SUBTILIS
Function / homology
Function and homology information


: / STAS domain / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Anti-sigma-factor antagonist (STAS) domain protein
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMarles-Wright, J. / Grant, T. / Delumeau, O. / van Duinen, G. / Firbank, S.J. / Lewis, P.J. / Murray, J.W. / Newman, J.A. / Quin, M.B. / Race, P.R. ...Marles-Wright, J. / Grant, T. / Delumeau, O. / van Duinen, G. / Firbank, S.J. / Lewis, P.J. / Murray, J.W. / Newman, J.A. / Quin, M.B. / Race, P.R. / Rohou, A. / Tichelaar, W. / van Heel, M. / Lewis, R.J.
CitationJournal: Science / Year: 2008
Title: Molecular architecture of the "stressosome," a signal integration and transduction hub.
Authors: Jon Marles-Wright / Tim Grant / Olivier Delumeau / Gijs van Duinen / Susan J Firbank / Peter J Lewis / James W Murray / Joseph A Newman / Maureen B Quin / Paul R Race / Alexis Rohou / Willem ...Authors: Jon Marles-Wright / Tim Grant / Olivier Delumeau / Gijs van Duinen / Susan J Firbank / Peter J Lewis / James W Murray / Joseph A Newman / Maureen B Quin / Paul R Race / Alexis Rohou / Willem Tichelaar / Marin van Heel / Richard J Lewis /
Abstract: A commonly used strategy by microorganisms to survive multiple stresses involves a signal transduction cascade that increases the expression of stress-responsive genes. Stress signals can be ...A commonly used strategy by microorganisms to survive multiple stresses involves a signal transduction cascade that increases the expression of stress-responsive genes. Stress signals can be integrated by a multiprotein signaling hub that responds to various signals to effect a single outcome. We obtained a medium-resolution cryo-electron microscopy reconstruction of the 1.8-megadalton "stressosome" from Bacillus subtilis. Fitting known crystal structures of components into this reconstruction gave a pseudoatomic structure, which had a virus capsid-like core with sensory extensions. We suggest that the different sensory extensions respond to different signals, whereas the conserved domains in the core integrate the varied signals. The architecture of the stressosome provides the potential for cooperativity, suggesting that the response could be tuned dependent on the magnitude of chemophysical insult.
History
DepositionJul 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTI-SIGMA-FACTOR ANTAGONIST
B: ANTI-SIGMA-FACTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)27,5372
Polymers27,5372
Non-polymers00
Water75742
1
A: ANTI-SIGMA-FACTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)13,7691
Polymers13,7691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ANTI-SIGMA-FACTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)13,7691
Polymers13,7691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.081, 60.418, 89.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANTI-SIGMA-FACTOR ANTAGONIST / MTS / STAS DOMAIN PROTEIN


Mass: 13768.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MOORELLA THERMOACETICA (bacteria) / Description: DSM / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q2RIF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS-TRIS PROPANE PH 6.5, 20%(W/V) PEG 3350

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 2.3→19.1 Å / Num. obs: 12304 / % possible obs: 97.2 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→19.06 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU B: 21.491 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28 593 4.8 %RANDOM
Rwork0.226 ---
obs0.228 11710 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 0 42 1810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221788
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9992422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5095228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99925.31364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53615342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.784158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021238
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6361.51138
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20921842
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0353650
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1754.5580
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.424 51
Rwork0.322 841
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1261-1.62522.1066.24732.81876.2662-0.04790.44560.1606-0.30370.0063-0.3537-0.23690.15990.04150.0854-0.00840.00990.0762-0.01770.079735.84036.0725.4346
24.4759-2.15210.00893.01641.14746.27820.1429-0.00110.20020.17260.0619-0.3042-0.15380.3158-0.20480.0879-0.01640.02910.05190.01840.080822.842924.159841.3433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 120
2X-RAY DIFFRACTION2B6 - 120

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