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- PDB-5ttt: Sparse-restraint solution NMR structure of micelle-solubilized cy... -

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Basic information

Entry
Database: PDB / ID: 5ttt
TitleSparse-restraint solution NMR structure of micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4 refined by restrained Rosetta
ComponentsDegenerin mec-4
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


negative regulation of turning behavior involved in mating / Sensory perception of salty taste / Stimuli-sensing channels / positive regulation of detection of mechanical stimulus involved in sensory perception of touch / positive regulation of mechanosensory behavior / neuron projection membrane / detection of mechanical stimulus involved in sensory perception of touch / mechanosensory behavior / ligand-gated sodium channel activity / response to mechanical stimulus ...negative regulation of turning behavior involved in mating / Sensory perception of salty taste / Stimuli-sensing channels / positive regulation of detection of mechanical stimulus involved in sensory perception of touch / positive regulation of mechanosensory behavior / neuron projection membrane / detection of mechanical stimulus involved in sensory perception of touch / mechanosensory behavior / ligand-gated sodium channel activity / response to mechanical stimulus / sodium ion transmembrane transport / potassium ion transport / axon / membrane / plasma membrane
Similarity search - Function
Degenerin / : / Mechanosensory ion channel subunit mec-4/10 cytosolic domain / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsEverett, J.K. / Liu, G. / Mao, B. / Driscoll, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: To Be Published
Title: Sparse-restraint solution NMR structure of micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4 refined by restrained Rosetta
Authors: Everett, J.K. / Liu, G. / Mao, B. / Driscoll, M.A. / Montelione, G.T.
History
DepositionNov 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jun 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 1.4May 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: Degenerin mec-4


Theoretical massNumber of molelcules
Total (without water)13,2971
Polymers13,2971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250target function
RepresentativeModel #1lowest energy
DetailsMonomer as determined by light scatering

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Components

#1: Protein Degenerin mec-4 / Mechanosensory abnormality protein 4


Mass: 13296.793 Da / Num. of mol.: 1 / Fragment: residues 1-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mec-4, mec-13, T01C8.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P24612

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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
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CO
151isotropic13D HN(CO)CA
161isotropic12D 1H-1H NOESY
171isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-13C; U-15N; U-2H] micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4, 95% H2O/5% D2O
Details: 1.5 MM [U-100% 13C; U-100% 15N; 100% 2H; ILV METHYL 1H; FY RING 1H] MEC4, 25 MM SODIUM; PHOSPHATE, 5 MM ZWITTERGENT 3-12, 25 MM SODIUM CHLORIDE, 5MM TCEP, 95% H2O/5% D2O
Label: CND / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.5 mM
Component: micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4
Isotopic labeling: [U-13C; U-15N; U-2H]
Sample conditionsDetails: 1.5 MM [U-100% 13C; U-100% 15N; 100% 2H; ILV METHYL 1H; FY RING 1H] MEC4, 25 MM SODIUM; PHOSPHATE, 5 MM ZWITTERGENT 3-12, 25 MM SODIUM CHLORIDE, 5MM TCEP, 95% H2O/5% D2O
Ionic strength: 0.025 M / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Restrained RosettaMao, Baker, Montelionerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
SparkyGoddardpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 250 / Conformers submitted total number: 20

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