6SA9

Endogenous Retrovirus HML2 Capsid NTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for Fullerene geometry in a human endogenous retrovirus capsid.

Acton, O.Grant, T.Nicastro, G.Ball, N.J.Goldstone, D.C.Robertson, L.E.Sader, K.Nans, A.Ramos, A.Stoye, J.P.Taylor, I.A.Rosenthal, P.B.

(2019) Nat Commun 10: 5822-5822

  • DOI: 10.1038/s41467-019-13786-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle ...

    The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute of Structural and Molecular Biology, University College London, London, UK.,Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. Ian.Taylor@crick.ac.uk.,Department of Medicine, Imperial College London, London, SW7 2AZ, UK.,Division of Molecular Structure, MRC National Institute for Medical Research, London, NW7 1AA, UK.,Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. Peter.Rosenthal@crick.ac.uk.,School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA.,Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Thermo Fisher Scientific Materials and Structural Analysis, Eindhoven, Netherlands.,Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endogenous retrovirus group K member 9 Pol protein
A, B
160Homo sapiensMutation(s): 0 
Gene Names: ERVK-9
Find proteins for P63128 (Homo sapiens)
Go to UniProtKB:  P63128
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 42.387α = 90.00
b = 98.920β = 94.37
c = 76.508γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited Kingdom--

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release