6SV2

Human prion protein (PrP) fragment 119-231 (G127V M129 variant) complexed to ICSM 18 (anti-Prp therapeutic antibody) Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural effects of the highly protective V127 polymorphism on human prion protein.

Hosszu, L.L.P.Conners, R.Sangar, D.Batchelor, M.Sawyer, E.B.Fisher, S.Cliff, M.J.Hounslow, A.M.McAuley, K.Leo Brady, R.Jackson, G.S.Bieschke, J.Waltho, J.P.Collinge, J.

(2020) Commun Biol 3: 402-402

  • DOI: https://doi.org/10.1038/s42003-020-01126-6
  • Primary Citation of Related Structures:  
    6SUZ, 6SV2

  • PubMed Abstract: 

    Prion diseases, a group of incurable, lethal neurodegenerative disorders of mammals including humans, are caused by prions, assemblies of misfolded host prion protein (PrP). A single point mutation (G127V) in human PrP prevents prion disease, however the structural basis for its protective effect remains unknown. Here we show that the mutation alters and constrains the PrP backbone conformation preceding the PrP β-sheet, stabilising PrP dimer interactions by increasing intermolecular hydrogen bonding. It also markedly changes the solution dynamics of the β2-α2 loop, a region of PrP structure implicated in prion transmission and cross-species susceptibility. Both of these structural changes may affect access to protein conformers susceptible to prion formation and explain its profound effect on prion disease.


  • Organizational Affiliation

    MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAINA [auth L]212Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAINB [auth H]215Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Major prion proteinC [auth A]113Homo sapiensMutation(s): 1 
Gene Names: PRNPALTPRPPRIPPRP
UniProt & NIH Common Fund Data Resources
Find proteins for P04156 (Homo sapiens)
Explore P04156 
Go to UniProtKB:  P04156
PHAROS:  P04156
GTEx:  ENSG00000171867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04156
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth H]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.076α = 90
b = 128.076β = 90
c = 135.642γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2020-07-29 
  • Deposition Author(s): Conners, R.

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_UU_00024/6

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description