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- PDB-2l9g: Solution structure of AS1p-Tar in 10% negatively charged bicelles -

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Basic information

Entry
Database: PDB / ID: 2l9g
TitleSolution structure of AS1p-Tar in 10% negatively charged bicelles
ComponentsMethyl-accepting chemotaxis protein II
KeywordsMEMBRANE PROTEIN / HAMP-domain / signal transduction / transmembrane communication / helicity of AS1 / membrane-spanning receptors
Function / homology
Function and homology information


detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / protein histidine kinase binding / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis ...detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / protein histidine kinase binding / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis / transmembrane signaling receptor activity / signal transduction / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain ...Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 9
AuthorsUnnerstale, S. / von Heijne, G. / Draheim, R.R. / Maler, L.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Structural characterization of AS1-membrane interactions from a subset of HAMP domains
Authors: Unnerstale, S. / Maler, L. / Draheim, R.R.
History
DepositionFeb 9, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein II


Theoretical massNumber of molelcules
Total (without water)2,1211
Polymers2,1211
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)25 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Methyl-accepting chemotaxis protein II / MCP-II / Aspartate chemoreceptor protein


Mass: 2120.647 Da / Num. of mol.: 1
Fragment: peptide AS1p-Tar from HAMP domain, UNP residues 214-232
Source method: obtained synthetically
Details: Obtained from PolyPeptide Group (Strasbourg, France) and were used without further purification.
Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P07017

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of AS1p-Tar in 10% negatively charged bicelles
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 50mM sodium phosphate; 240mM [U-2H] DHPC; 54mM [U-2H] DMPC; 6mM [U-2H] DMPG; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
240 mMDHPC-2[U-2H]1
54 mMDMPC-3[U-2H]1
6 mMDMPG-4[U-2H]1
Sample conditionsIonic strength: 0.05 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 133 / NOE intraresidue total count: 59 / NOE medium range total count: 33 / NOE sequential total count: 41
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0.15 Å / Maximum upper distance constraint violation: 0.19 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 1.04 Å / Distance rms dev error: 0.36 Å

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