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- PDB-6lni: Cryo-EM structure of amyloid fibril formed by full-length human p... -

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Basic information

Entry
Database: PDB / ID: 6lni
TitleCryo-EM structure of amyloid fibril formed by full-length human prion protein
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / Amyloid fibril
Function / homology
Function and homology information


negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding ...negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of interleukin-2 production / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / cuprous ion binding / negative regulation of amyloid-beta formation / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / inclusion body / neuron projection maintenance / tubulin binding / positive regulation of calcium-mediated signaling / cellular response to copper ion / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to xenobiotic stimulus / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / signaling receptor activity / protein-folding chaperone binding / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / molecular adaptor activity / transmembrane transporter binding / learning or memory / postsynapse / regulation of cell cycle / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.702 Å
AuthorsWang, L.Q. / Zhao, K. / Yuan, H.Y. / Wang, Q. / Guan, Z.Y. / Tao, J. / Li, X.N. / Hao, M.M. / Chen, J. / Zhang, D.L. ...Wang, L.Q. / Zhao, K. / Yuan, H.Y. / Wang, Q. / Guan, Z.Y. / Tao, J. / Li, X.N. / Hao, M.M. / Chen, J. / Zhang, D.L. / Zhu, H.L. / Yin, P. / Liu, C. / Liang, Y.
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structure of an amyloid fibril formed by full-length human prion protein.
Authors: Li-Qiang Wang / Kun Zhao / Han-Ye Yuan / Qiang Wang / Zeyuan Guan / Jing Tao / Xiang-Ning Li / Yunpeng Sun / Chuan-Wei Yi / Jie Chen / Dan Li / Delin Zhang / Ping Yin / Cong Liu / Yi Liang /
Abstract: Prion diseases are caused by the misfolding of prion protein (PrP). Misfolded PrP forms protease-resistant aggregates in vivo (PrP) that are able to template the conversion of the native form of the ...Prion diseases are caused by the misfolding of prion protein (PrP). Misfolded PrP forms protease-resistant aggregates in vivo (PrP) that are able to template the conversion of the native form of the protein (PrP), a property shared by in vitro-produced PrP fibrils. Here we produced amyloid fibrils in vitro from recombinant, full-length human PrP (residues 23-231) and determined their structure using cryo-EM, building a model for the fibril core comprising residues 170-229. The PrP fibril consists of two protofibrils intertwined in a left-handed helix. Lys194 and Glu196 from opposing subunits form salt bridges, creating a hydrophilic cavity at the interface of the two protofibrils. By comparison with the structure of PrP, we propose that two α-helices in the C-terminal domain of PrP are converted into β-strands stabilized by a disulfide bond in the PrP fibril. Our data suggest that different PrP mutations may play distinct roles in modulating the conformational conversion.
History
DepositionDec 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
A: Major prion protein
B: Major prion protein
C: Major prion protein
D: Major prion protein
E: Major prion protein
F: Major prion protein
G: Major prion protein
H: Major prion protein
I: Major prion protein
J: Major prion protein


Theoretical massNumber of molelcules
Total (without water)229,96410
Polymers229,96410
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area42630 Å2
ΔGint-123 kcal/mol
Surface area27390 Å2

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Components

#1: Protein
Major prion protein / PrP / ASCR / PrP27-30 / PrP33-35C


Mass: 22996.355 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRNP, ALTPRP, PRIP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04156
Has protein modificationY
Sequence detailsRegarding the conflict, the Met residue is a part of the initiation codon of human prion protein ...Regarding the conflict, the Met residue is a part of the initiation codon of human prion protein (PrP) in prokaryotic expression system. (see SEQADV)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: human prion protein amyloid fibril / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.449 ° / Axial rise/subunit: 2.403 Å / Axial symmetry: C1
3D reconstructionResolution: 2.702 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86012 / Symmetry type: HELICAL

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