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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 | ||||||
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Title | Cryo-EM structure of amyloid fibril formed by full-length human prion protein | ||||||
![]() | Major prion protein | ||||||
![]() | PROTEIN FIBRIL / Amyloid fibril | ||||||
Function / homology | ![]() positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production ...positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / 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 / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / tubulin binding / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / postsynapse / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / transmembrane transporter binding / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / cell cycle / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.702 Å | ||||||
![]() | 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. ...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. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 129.6 KB | Display | ![]() |
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PDB format | ![]() | 99 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 692.4 KB | Display | ![]() |
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Full document | ![]() | 700.9 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 40.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0931MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 22996.355 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Sequence details | Regarding 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: human prion protein amyloid fibril / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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Helical symmerty | Angular rotation/subunit: 179.449 ° / Axial rise/subunit: 2.403 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 2.702 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86012 / Symmetry type: HELICAL |