6SAI | pdb_00006sai

NMR solution structure of Hml-2 C-terminal dimer domain

• PDB DOI: https://doi.org/10.2210/pdb6SAI/pdb
• BMRB: 34419

• Classification: VIRAL PROTEIN
• Organism(s): Human endogenous retrovirus K
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-16 Released: 2020-01-15 
• Deposition Author(s): Nicastro, G., Taylor, I.A., Ball, N.J., Ramos, A.
• Funding Organization(s): The Francis Crick Institute

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

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

• PubMed: 31862888 
• DOI: https://doi.org/10.1038/s41467-019-13786-y
• Primary Citation Related Structures: 
  6SA9, 6SAI, 6SSJ, 6SSK, 6SSL, 6SSM


• 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 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: 
• Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
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.
School of Biological Sciences, University of Auckland, Auckland, New Zealand.
Thermo Fisher Scientific Materials and Structural Analysis, Eindhoven, Netherlands.
Division of Molecular Structure, MRC National Institute for Medical Research, London, NW7 1AA, UK.
Institute of Structural and Molecular Biology, University College London, London, UK.
Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
Department of Medicine, Imperial College London, London, SW7 2AZ, UK.
Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. [e-mail].
Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.19 kDa 
• Atom Count: 1,408 
• Modeled Residue Count: 186 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag protein	A, B	93	Human endogenous retrovirus K	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for P87891 (Human endogenous retrovirus K) Explore P87891  Go to UniProtKB:  P87891

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Nicastro, G., Taylor, I.A., Ball, N.J., Ramos, A.

---

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC001178

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references