6HAU

KSHV PAN RNA Mta-response element fragment complexed with the globular domain of herpesvirus saimiri ORF57

• PDB DOI:  https://doi.org/10.2210/pdb6HAU/pdb
• NAKB: 6HAU

• Classification: RNA BINDING PROTEIN
• Organism(s): Herpesvirus saimiri (strain 11), Human gammaherpesvirus 8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-08 Released: 2018-11-21 
• Deposition Author(s): Tunnicliffe, R.B., Levy, C., Ruiz Nivia, H.D., Sandri-Goldin, R.M., Golovanov, A.P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.197 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Structural identification of conserved RNA binding sites in herpesvirus ORF57 homologs: implications for PAN RNA recognition.

Tunnicliffe, R.B., Levy, C., Ruiz Nivia, H.D., Sandri-Goldin, R.M., Golovanov, A.P.

(2019) Nucleic Acids Res 47: 1987-2001

• PubMed: 30462297 
• DOI: https://doi.org/10.1093/nar/gky1181
• Primary Citation of Related Structures:  
  6HAT, 6HAU


• PubMed Abstract: 
  

Kaposi's sarcoma-associated herpesvirus (KSHV) transcribes a long noncoding polyadenylated nuclear (PAN) RNA, which promotes the latent to lytic transition by repressing host genes involved in antiviral responses as well as viral proteins that support the latent state. KSHV also expresses several early proteins including ORF57 (Mta), a member of the conserved multifunctional ICP27 protein family, which is essential for productive replication. ORF57/Mta interacts with PAN RNA via a region termed the Mta responsive element (MRE), stabilizing the transcript and supporting nuclear accumulation. Here, using a close homolog of KSHV ORF57 from herpesvirus saimiri (HVS), we determined the crystal structure of the globular domain in complex with a PAN RNA MRE, revealing a uracil specific binding site that is also conserved in KSHV. Using solution NMR, RNA binding was also mapped within the disordered N-terminal domain of KSHV ORF57, and showed specificity for an RNA fragment containing a GAAGRG motif previously known to bind a homologous region in HVS ORF57. Together these data located novel differential RNA recognition sites within neighboring domains of herpesvirus ORF57 homologs, and revealed high-resolution details of their interactions with PAN RNA, thus providing insight into interactions crucial to viral function.

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Organizational Affiliation: 

Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
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: 67.05 kDa 
• Atom Count: 5,002 
• Modelled Residue Count: 552 
• Deposited Residue Count: 563 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA export factor ICP27 homolog	A, B	273	Herpesvirus saimiri (strain 11)	Mutation(s): 0  Gene Names: EJRF1, ORF57
UniProt
Find proteins for P13199 (Saimiriine herpesvirus 2 (strain 11)) Explore P13199  Go to UniProtKB:  P13199

Entity ID: 2
Molecule	Chains	Length	Organism	Image
MRE fragment of PAN RNA	C [auth D]	17	Human gammaherpesvirus 8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.197 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.657	α = 90
b = 105.261	β = 90
c = 118.554	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Tunnicliffe, R.B., Levy, C., Ruiz Nivia, H.D., Sandri-Goldin, R.M., Golovanov, A.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI107803

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references
• Version 1.2: 2019-03-13
  Changes: Data collection, Database references
• Version 1.3: 2019-04-10
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2022-03-30
  Changes: Author supporting evidence, Database references