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- PDB-2l8t: Staphylococcus aureus pathogenicity island 1 protein gp6, an inte... -

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Basic information

Entry
Database: PDB / ID: 2l8t
TitleStaphylococcus aureus pathogenicity island 1 protein gp6, an internal scaffold in size determination
ComponentsTransposon Tn557 toxic shock syndrome toxin-1
KeywordsSTRUCTURAL PROTEIN / scaffold / bacteriophage / sapi
Function / homologyGTP Cyclohydrolase I; Chain A, domain 1 - #40 / Pathogenicity island protein gp6, Staphylococcus / Pathogenicity island protein gp6 superfamily / Pathogenicity island protein gp6 in Staphylococcus / GTP Cyclohydrolase I; Chain A, domain 1 / Helix non-globular / Special / Hypothetical mobile element-associated protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsDearborn, A.D. / Spilman, M.S. / Damle, P.K. / Chang, J.R. / Monroe, E.B. / Saad, J.S. / Christie, G.E. / Dokland, T.
CitationJournal: J Mol Biol / Year: 2011
Title: The Staphylococcus aureus pathogenicity island 1 protein gp6 functions as an internal scaffold during capsid size determination.
Authors: Altaira D Dearborn / Michael S Spilman / Priyadarshan K Damle / Jenny R Chang / Eric B Monroe / Jamil S Saad / Gail E Christie / Terje Dokland /
Abstract: Staphylococcus aureus pathogenicity island 1 (SaPI1) is a mobile genetic element that carries genes for several superantigen toxins. SaPI1 is normally stably integrated into the host genome but can ...Staphylococcus aureus pathogenicity island 1 (SaPI1) is a mobile genetic element that carries genes for several superantigen toxins. SaPI1 is normally stably integrated into the host genome but can become mobilized by "helper" bacteriophage 80α, leading to the packaging of SaPI1 genomes into phage-like transducing particles that are composed of structural proteins supplied by the helper phage but having smaller capsids. We show that the SaPI1-encoded protein gp6 is necessary for efficient formation of small capsids. The NMR structure of gp6 reveals a dimeric protein with a helix-loop-helix motif similar to that of bacteriophage scaffolding proteins. The gp6 dimer matches internal densities that bridge capsid subunits in cryo-electron microscopy reconstructions of SaPI1 procapsids, suggesting that gp6 acts as an internal scaffolding protein in capsid size determination.
History
DepositionJan 24, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transposon Tn557 toxic shock syndrome toxin-1
B: Transposon Tn557 toxic shock syndrome toxin-1


Theoretical massNumber of molelcules
Total (without water)16,3002
Polymers16,3002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transposon Tn557 toxic shock syndrome toxin-1 / Pathogenicity island 1 protein gp6


Mass: 8150.040 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O54465

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1423D HN(COCA)CB
1523D HN(CO)CA
1623D HNCA
1723D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 15N] protein, 10 mM sodium phosphate, 200 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] protein, 10 mM sodium phosphate, 200 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-99% 15N]1
10 mMsodium phosphate-21
200 mMsodium chloride-31
1 mMprotein-4[U-99% 13C; U-99% 15N]2
10 mMsodium phosphate-52
200 mMsodium chloride-62
Sample conditionsIonic strength: 200 / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Ultrashield Plus / Manufacturer: Bruker / Model: Ultrashield Plus / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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