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- PDB-2m5k: Atomic-resolution structure of a doublet cross-beta amyloid fibril -

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Basic information

Entry
Database: PDB / ID: 2m5k
TitleAtomic-resolution structure of a doublet cross-beta amyloid fibril
ComponentsTransthyretin
KeywordsPROTEIN FIBRIL / amyloid fibril / cross-beta structure
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / 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 / ELECTRON MICROSCOPY / single particle reconstruction / simulated annealing / cryo EM / Resolution: 12.7 Å
Model detailslowest energy, model1
AuthorsFitzpatrick, A.W.P. / Debelouchina, G.T. / Bayro, M.J. / Clare, D.K. / Caporini, M.A. / Bajaj, V.S. / Jaroniec, C.P. / Wang, L. / Ladizhansky, V. / Muller, S. ...Fitzpatrick, A.W.P. / Debelouchina, G.T. / Bayro, M.J. / Clare, D.K. / Caporini, M.A. / Bajaj, V.S. / Jaroniec, C.P. / Wang, L. / Ladizhansky, V. / Muller, S. / MacPhee, C.E. / Waudby, C.A. / Mott, H.R. / de Simone, A. / Knowles, T.P.J. / Saibil, H.R. / Vendruscolo, M. / Orlova, E.V. / Griffin, R.G. / Dobson, C.M.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic structure and hierarchical assembly of a cross-β amyloid fibril.
Authors: Anthony W P Fitzpatrick / Galia T Debelouchina / Marvin J Bayro / Daniel K Clare / Marc A Caporini / Vikram S Bajaj / Christopher P Jaroniec / Luchun Wang / Vladimir Ladizhansky / Shirley A ...Authors: Anthony W P Fitzpatrick / Galia T Debelouchina / Marvin J Bayro / Daniel K Clare / Marc A Caporini / Vikram S Bajaj / Christopher P Jaroniec / Luchun Wang / Vladimir Ladizhansky / Shirley A Müller / Cait E MacPhee / Christopher A Waudby / Helen R Mott / Alfonso De Simone / Tuomas P J Knowles / Helen R Saibil / Michele Vendruscolo / Elena V Orlova / Robert G Griffin / Christopher M Dobson /
Abstract: The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have ...The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale--including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy--we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils.
History
DepositionFeb 27, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.2Feb 26, 2020Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_cs
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status / pdbx_struct_oper_list
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_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.4Apr 17, 2024Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.status_code_mr
Revision 1.5May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin


Theoretical massNumber of molelcules
Total (without water)9,5878
Polymers9,5878
Non-polymers00
Water00
1
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin
x 114


Theoretical massNumber of molelcules
Total (without water)1,092,910912
Polymers1,092,910912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation113
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 114 / Rise per n subunits: 4.67 Å / Rotation per n subunits: -0.85 °)

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Components

#1: Protein/peptide
Transthyretin / Prealbumin / TBPA


Mass: 1198.366 Da / Num. of mol.: 8 / Fragment: UNP residues 125-135 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P02767

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Experimental details

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Experiment

Experiment
Method
SOLID-STATE NMR
ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D DQ-DRAWS
121REDOR
131ZF-TEDOR
1412D PDSD

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Sample preparation

ComponentName: Doublet cross-beta amyloid fibril polymorph / Type: COMPLEX
Buffer solutionName: 10% acetonitrile/water / pH: 2 / Details: 10% acetonitrile/water
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon films (R2/2, QuantifoilMicro Tools GmbH, Jena, Germany)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 99 K / Humidity: 95 %
Details: Fibrils were applied to holey carbon films that were immediately plunge-frozen at liquid nitrogen temperature.
DetailsContents: 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115), 10% acetonitrile/water solution
Solvent system: 10% acetonitrile/water solution
SampleConc.: 15 mg/mL / Component: TTR(105-115)-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 2 / Pressure: ambient / Temperature units: K

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Mar 3, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 40000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 99 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 250
NMR spectrometer
TypeManufacturerField strength (MHz)Spectrometer-ID
BrukerBruker9001
7502
5003

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Processing

EM software
IDNameCategory
1BKRP3D reconstruction
2IMAGIC3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: CTFFIND3
3D reconstructionMethod: Common crossovers / Resolution: 12.7 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 82 / Nominal pixel size: 1.8 Å / Actual pixel size: 1.8 Å
Details: The particles were selected using an automatic selection program.
Num. of class averages: 18 / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms680 0 0 0 680
NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 1

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