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- PDB-3zpk: Atomic-resolution structure of a quadruplet cross-beta amyloid fibril. -

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Entry
Database: PDB / ID: 3zpk
TitleAtomic-resolution structure of a quadruplet cross-beta amyloid fibril.
ComponentsTRANSTHYRETIN
KeywordsPROTEIN 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 / CNSSOLVE / cryo EM
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.A. ...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.A. / 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 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Experimental preparation
Revision 2.0Mar 21, 2018Group: Atomic model / Derived calculations / Experimental preparation
Category: atom_site / em_sample_support / pdbx_struct_assembly
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_sample_support.grid_type / _pdbx_struct_assembly.details
Revision 2.1Nov 18, 2020Group: Refinement description / Category: refine / Item: _refine.pdbx_refine_id
Revision 2.2Jan 27, 2021Group: Derived calculations / Structure summary / Category: audit_author / pdbx_struct_oper_list
Item: _audit_author.name / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.type
Revision 2.3Feb 3, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

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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
I: TRANSTHYRETIN
J: TRANSTHYRETIN
K: TRANSTHYRETIN
L: TRANSTHYRETIN
M: TRANSTHYRETIN
N: TRANSTHYRETIN
O: TRANSTHYRETIN
P: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)19,17416
Polymers19,17416
Non-polymers00
Water0
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
C: TRANSTHYRETIN
D: TRANSTHYRETIN
E: TRANSTHYRETIN
F: TRANSTHYRETIN
G: TRANSTHYRETIN
H: TRANSTHYRETIN
I: TRANSTHYRETIN
J: TRANSTHYRETIN
K: TRANSTHYRETIN
L: TRANSTHYRETIN
M: TRANSTHYRETIN
N: TRANSTHYRETIN
O: TRANSTHYRETIN
P: TRANSTHYRETIN
x 114


Theoretical massNumber of molelcules
Total (without water)2,185,8201824
Polymers2,185,8201824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
helical symmetry operation113
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative
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: -0.89 °)

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Components

#1: Protein/peptide
TRANSTHYRETIN / / PREALBUMIN / TBPA


Mass: 1198.366 Da / Num. of mol.: 16 / Fragment: 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

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Sample preparation

ComponentName: Quadruplet cross-beta amyloid fibril polymorph / Type: COMPLEX
Buffer solutionpH: 2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Holey carbon films R2/2 Quantifoil / Grid type: R2/2 Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansScanner model: ZEISS SCAI
Radiation wavelengthRelative weight: 1

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Processing

3D reconstructionNum. of particles: 175 / Symmetry type: HELICAL
RefinementMethod to determine structure: CNSSOLVE
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 0 0 1360
NMR ensembleConformers submitted total number: 1

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