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- PDB-2nbp: Solution structure of the T119M variant of transthyretin in its m... -

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Basic information

Entry
Database: PDB / ID: 2nbp
TitleSolution structure of the T119M variant of transthyretin in its monomeric state
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / amyloid / aggregation / monomer
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKim, J. / Oroz, J. / Zweckstetter, M.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2016
Title: Structure of Monomeric Transthyretin Carrying the Clinically Important T119M Mutation.
Authors: Kim, J.H. / Oroz, J. / Zweckstetter, M.
History
DepositionMar 9, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin


Theoretical massNumber of molelcules
Total (without water)13,8101
Polymers13,8101
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13809.512 Da / Num. of mol.: 1 / Mutation: F107M, L130M, T139M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / Variant (production host): pREP4 / References: UniProt: P02766

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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-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.6-1.2 mM [U-13C; U-15N] T119M M-TTR, 50 mM MES, 100 mM sodium chloride, 5 mM DTT, 0.1 mM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMT119M M-TTR-1[U-13C; U-15N]0.6-1.21
50 mMMES-21
100 mMsodium chloride-31
5 mMDTT-41
0.1 mMDSS-51
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Oxford AvanceOxfordAVANCE7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2238 / NOE intraresidue total count: 493 / NOE long range total count: 826 / NOE medium range total count: 254 / NOE sequential total count: 665 / Hydrogen bond constraints total count: 144 / Protein chi angle constraints total count: 24 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 97
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 3.52 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.3 Å / Maximum torsion angle constraint violation: 4.2 ° / Maximum upper distance constraint violation: 0.13 Å / Representative conformer: 1 / Torsion angle constraint violation method: rms
NMR ensemble rmsDistance rms dev: 0.0052 Å / Distance rms dev error: 0.0007 Å

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