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- PDB-6xfl: Structural characterization of the type III secretion system pilo... -

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Basic information

Entry
Database: PDB / ID: 6xfl
TitleStructural characterization of the type III secretion system pilotin-secretin complex InvH-InvG by NMR spectroscopy
Components
  • Type 3 secretion system pilotin
  • Type 3 secretion system secretin
KeywordsPROTEIN TRANSPORT / pilotin / secretin / chaperone / type III secretion
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
InvH outer membrane lipoprotein / InvH outer membrane lipoprotein / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily ...InvH outer membrane lipoprotein / InvH outer membrane lipoprotein / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
SPI-1 type 3 secretion system pilotin / SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsMajewski, D.D. / Okon, M. / Heinkel, F. / Robb, C.S. / Vuckovic, M. / McIntosh, L.P. / Strynadka, N.C.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Structure / Year: 2021
Title: Characterization of the Pilotin-Secretin Complex from the Salmonella enterica Type III Secretion System Using Hybrid Structural Methods.
Authors: Majewski, D.D. / Okon, M. / Heinkel, F. / Robb, C.S. / Vuckovic, M. / McIntosh, L.P. / Strynadka, N.C.J.
History
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 3 secretion system pilotin
B: Type 3 secretion system secretin


Theoretical massNumber of molelcules
Total (without water)14,7022
Polymers14,7022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein Type 3 secretion system pilotin / Invasion lipoprotein invH


Mass: 9453.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: invH, sctG, STM2900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CL43
#2: Protein/peptide Type 3 secretion system secretin / T3SS secretin / Protein InvG


Mass: 5248.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: sctC, invG, STM2898 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35672

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
161isotropic13D HNCO
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CO
151isotropic13D (H)CCH-TOCSY
171isotropic13D HCC(CO)NH-TOCSY
1121isotropic12D 1H-13C HSQC
1111isotropic13D HBHA(CBCACO)NH
1101isotropic13D (HB)CB(CGCD)HD
191isotropic13D (HB)CB(CGCDCE)HE
181isotropic13D hbCBcgcCH
1211isotropic13D 1H-13C NOESY
1201isotropic13D 1H-15N NOESY
1191isotropic13D 1H-13C NOESY filtered-edited
1181isotropic13D 1H-15N NOESY filtered-edited
1172isotropic22D 1H-15N HSQC
1162isotropic23D HNCO
1152isotropic23D HN(CA)CB
1312isotropic23D CBCA(CO)NH
1302isotropic13D HN(CA)CO
1292isotropic13D (H)CCH-TOCSY
1282isotropic13D HCC(CO)NH-TOCSY
1272isotropic12D 1H-13C HSQC
1262isotropic13D HBHA(CBCACO)NH
1252isotropic13D (HB)CB(CGCD)HD
1242isotropic13D (HB)CB(CGCDCE)HE
1232isotropic13D hbCBcgcCH
1222isotropic23D 1H-13C NOESY aliphatic
1142isotropic23D 1H-13C NOESY aromatic
1132isotropic23D 1H-15N NOESY
1332isotropic13D 1H-13C NOESY filtered-edited
1322isotropic13D 1H-15N NOESY filtered-edited

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM NA- MOPS, 150 mM NA- sodium chloride, 0.2 mM NA- TCEP, 10 % v/v NA- D2O, 90% H2O/10% D2O13C-15N-InvH, Unlabelled InvG90% H2O/10% D2O
solution220 mM NA- MOPS, 150 mM NA- sodium chloride, 0.2 mM NA- TCEP, 10 % v/v NA- D2O, 90% H2O/10% D2OUnlabelled InvH, C13-N15-InvG90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMOPSNA-1
150 mMsodium chlorideNA-1
0.2 mMTCEPNA-1
10 % v/vD2ONA-1
20 mMMOPSNA-2
150 mMsodium chlorideNA-2
0.2 mMTCEPNA-2
10 % v/vD2ONA-2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert P.refinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
Refinement
MethodSoftware ordinal
simulated annealing2
torsion angle dynamics1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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