6PQ5

AGAAAA segment 113-118 from human prion

  • Classification: PROTEIN FIBRIL
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2019-07-08 Released: 2020-04-15 
  • Deposition Author(s): Apostol, M.I., Sawaya, M.R., Eisenberg, D.
  • Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core.

Glynn, C.Sawaya, M.R.Ge, P.Gallagher-Jones, M.Short, C.W.Bowman, R.Apostol, M.Zhou, Z.H.Eisenberg, D.S.Rodriguez, J.A.

(2020) Nat Struct Mol Biol 27: 417-423

  • DOI: 10.1038/s41594-020-0403-y
  • Primary Citation of Related Structures:  
    6PQ5, 6PQA, 6UUR

  • PubMed Abstract: 
  • Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein ...

    Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein. This human prion fibril contains two protofilaments intertwined with screw symmetry and linked by a tightly packed hydrophobic interface. Each protofilament consists of an extended beta arch formed by residues 106 to 145 of the prion protein, a hydrophobic and highly fibrillogenic disease-associated segment. Such structures of prion polymorphs serve as blueprints on which to evaluate the potential impact of sequence variants on prion disease.


    Organizational Affiliation

    Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA. jrodriguez@mbi.ucla.edu.



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major prion proteinA, B6Homo sapiensMutation(s): 0 
Gene Names: PRNPALTPRPPRIPPRP
UniProt & NIH Common Fund Data Resources
Find proteins for P04156 (Homo sapiens)
Explore P04156 
Go to UniProtKB:  P04156
PHAROS:  P04156
Entity Groups  
UniProt GroupP04156
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 18.533α = 90
b = 9.508β = 120.54
c = 17.632γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01 AG029430
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01 AG029430-05
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM007185
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM007185

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2020-05-27
    Changes: Database references