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- PDB-1rvs: STRUCTURE OF TRANSTHYRETIN IN AMYLOID FIBRILS DETERMINED BY SOLID... -

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Basic information

Entry
Database: PDB / ID: 1rvs
TitleSTRUCTURE OF TRANSTHYRETIN IN AMYLOID FIBRILS DETERMINED BY SOLID-STATE MAGIC ANGLE SPINNING NMR
ComponentsTransthyretin
KeywordsDE NOVO PROTEIN / TRANSTHYRETIN / TTR / AMYLOID / FIBRIL
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / extracellular region / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLID-STATE NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsJaroniec, C.P. / Macphee, C.E. / Bajaj, V.S. / Mcmahon, M.T. / Dobson, C.M. / Griffin, R.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy
Authors: Jaroniec, C.P. / MacPhee, C.E. / Bajaj, V.S. / McMahon, M.T. / Dobson, C.M. / Griffin, R.G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Molecular Conformation of a Peptide Fragment of Transthyretin in an Amyloid Fibril
Authors: Jaroniec, C.P. / MacPhee, C.E. / Astrof, N.S. / Dobson, C.M. / Griffin, R.G.
History
DepositionDec 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 7, 2021Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_entity_src_syn / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_spectrometer.manufacturer
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)1,1981
Polymers1,1981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Transthyretin / Prealbumin / TBPA


Mass: 1198.366 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-11 / Source method: obtained synthetically
Details: THE PEPTIDE WAS SYNTHESIZED BY STANDARD SOLID-PHASE METHODS AND HPLC PURIFICATION.
Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P02767

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D-TEDOR
1212D-FS-REDOR
1313D-N-C-C-N
1413D-H-N-C-H

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Sample preparation

DetailsContents: TRANSTHYRETIN AMYLOID FIBRILS
Sample conditionsPressure: AMBIENT / Temperature: 275.15 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerManufacturer: Home-built / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGERrefinement
RNMRRUBENcollection
RNMRRUBENdata analysis
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
Details: IN ADDITION TO EXPERIMENTAL NMR RESTRAINTS, BACKBONE CONFORMATION INDEPENDENT DATABASE-DERIVED RESTRAINTS (DUNBRACK, R.L. AND KARPLUS, M.J., J.MOL.BIOL. 1993, 203:543-574) WERE USED TO ...Details: IN ADDITION TO EXPERIMENTAL NMR RESTRAINTS, BACKBONE CONFORMATION INDEPENDENT DATABASE-DERIVED RESTRAINTS (DUNBRACK, R.L. AND KARPLUS, M.J., J.MOL.BIOL. 1993, 203:543-574) WERE USED TO UNIQUELY DEFINE THE SIDE-CHAIN CONFORMATION OF TYR AND LEU RESIDUES
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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