1ZLA

X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA.

Barbera, A.J.Chodaparambil, J.V.Kelley-Clarke, B.Joukov, V.Walter, J.C.Luger, K.Kaye, K.M.

(2006) Science 311: 856-861

  • DOI: 10.1126/science.1120541
  • Primary Citation of Related Structures:  
    1ZLA

  • PubMed Abstract: 
  • Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) mediates viral genome attachment to mitotic chromosomes. We find that N-terminal LANA docks onto chromosomes by binding nucleosomes through the folded region of histones H2A-H2B ...

    Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) mediates viral genome attachment to mitotic chromosomes. We find that N-terminal LANA docks onto chromosomes by binding nucleosomes through the folded region of histones H2A-H2B. The same LANA residues were required for both H2A-H2B binding and chromosome association. Further, LANA did not bind Xenopus sperm chromatin, which is deficient in H2A-H2B; chromatin binding was rescued after assembly of nucleosomes containing H2A-H2B. We also describe the 2.9-angstrom crystal structure of a nucleosome complexed with the first 23 LANA amino acids. The LANA peptide forms a hairpin that interacts exclusively with an acidic H2A-H2B region that is implicated in the formation of higher order chromatin structure. Our findings present a paradigm for how nucleosomes may serve as binding platforms for viral and cellular proteins and reveal a previously unknown mechanism for KSHV latency.


    Organizational Affiliation

    Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
histone H3C [auth A],
G [auth E]
135Xenopus laevisMutation(s): 2 
Gene Names: Histone H3
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Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
102Xenopus laevisMutation(s): 0 
Gene Names: Histone H4
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Xenopus laevis-like histone H2AE [auth C],
I [auth G]
129Expression vector pET3-H2AMutation(s): 3 
Gene Names: Histone H2A
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
histone H2BF [auth D],
J [auth H]
125Xenopus laevisMutation(s): 0 
Gene Names: Histone H2B
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
latent nuclear antigenK22N/AMutation(s): 0 
UniProt
Find proteins for Q9DUM3 (Human herpesvirus 8)
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UniProt GroupQ9DUM3
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Palindromic 146bp Human alpha-Satellite DNA fragmentA [auth I],
B [auth J]
146Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.162α = 90
b = 109.599β = 90
c = 182.237γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Structure summary
  • Version 1.4: 2021-10-20
    Changes: Database references