8Q36

Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Viral peptide conjugates for metal-warhead delivery to chromatin.

Batchelor, L.K.De Falco, L.Dyson, P.J.Davey, C.A.

(2024) RSC Adv 14: 8718-8725

  • DOI: https://doi.org/10.1039/d4ra01617c
  • Primary Citation of Related Structures:  
    8Q36, 8Q3E, 8Q3M, 8Q3X

  • PubMed Abstract: 

    The presence of heavy metal groups can endow compounds with unique structural and chemical attributes beneficial for developing highly potent therapeutic agents and effective molecular labels. However, metallocompound binding site specificity is a major challenge that dictates the level of off-site targeting, which is a limiting factor in finding safer and more effective metal-based drugs. Here we designed and tested a family of metallopeptide conjugates based on two different chromatin-tethering viral proteins and a drug being repurposed for cancer, the Au(i) anti-arthritic auranofin. The viral peptides associate with the acidic patch of the nucleosome while the gold moiety can bind allosterically to the H3 H113 imidazole. To achieve synthesis of the conjugates, we also engineered a sulfur-free, nucleosome-binding Kaposi's sarcoma herpesvirus LANA peptide with a methionine-to-ornithine substitution and coupled the peptide to the metal group in a final step using click chemistry. The four conjugates tested are all selectively cytotoxic towards tumor cell lines, but the choice of viral peptide and mode of linkage to the Au(i) group influences metal binding site preference. Our findings suggest that viral peptide-metalloconjugates have potential for use in chromatin delivery of therapeutic warheads and as nucleosome-specific tags.


  • Organizational Affiliation

    Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland paul.dyson@epfl.ch.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GAG structural proteinA [auth MMM]18Human spumaretrovirusMutation(s): 0 
UniProt
Find proteins for P14349 (Human spumaretrovirus)
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Go to UniProtKB:  P14349
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UniProt GroupP14349
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1B [auth AAA],
F [auth EEE]
98Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth BBB],
G [auth FFF]
87Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/ED [auth CCC],
H [auth GGG]
107Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-KE [auth DDD],
I [auth HHH]
95Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens)
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)J [auth III]145Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (145-MER)K [auth JJJ]145Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth EEE]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.194α = 90
b = 109.563β = 90
c = 183.675γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeMOE2015-T2-2-089
Ministry of Education (MoE, Singapore)SingaporeMOE-T2EP30121-0005
Ministry of Education (MoE, Singapore)Singapore2017-T1-002-020
Ministry of Education (MoE, Singapore)Singapore2020-T1-001-128
Ministry of Education (MoE, Singapore)Singapore2021-T1-001-014

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release