4BLG | pdb_00004blg

Crystal structure of MHV-68 Latency-associated nuclear antigen (LANA) C-terminal DNA binding domain

PDB DOI: https://doi.org/10.2210/pdb4BLG/pdb

Classification: VIRAL PROTEIN
Organism(s): Murid gammaherpesvirus 4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-02 Released: 2013-10-30
Deposition Author(s): Correia, B., Cerqueira, S.A., Beauchemin, C., Pires De Miranda, M., Li, S., Ponnusamy, R., Rodrigues, L., Schneider, T.R., Carrondo, M.A., Kaye, K.M., Simas, J.P., McVey, C.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.203 (Depositor), 0.212 (DCC)
R-Value Work:
0.171 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Gamma-2 Herpesvirus Lana DNA Binding Domain Identifies Charged Surface Residues which Impact Viral Latency

Correia, B., Cerqueira, S.A., Beauchemin, C., Pires De Miranda, M., Li, S., Ponnusamy, R., Rodrigues, L., Schneider, T.R., Carrondo, M.A., Kaye, K.M., Simas, J.P., Mcvey, C.E.

(2013) PLoS Pathog 9: 3673

PubMed: 24146618 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1003673
Primary Citation Related Structures:
4BLG

PubMed Abstract:
Latency-associated nuclear antigen (LANA) mediates γ2-herpesvirus genome persistence and regulates transcription. We describe the crystal structure of the murine gammaherpesvirus-68 LANA C-terminal domain at 2.2 Å resolution. The structure reveals an alpha-beta fold that assembles as a dimer, reminiscent of Epstein-Barr virus EBNA1. A predicted DNA binding surface is present and opposite this interface is a positive electrostatic patch. Targeted DNA recognition substitutions eliminated DNA binding, while certain charged patch mutations reduced bromodomain protein, BRD4, binding. Virus containing LANA abolished for DNA binding was incapable of viable latent infection in mice. Virus with mutations at the charged patch periphery exhibited substantial deficiency in expansion of latent infection, while central region substitutions had little effect. This deficiency was independent of BRD4. These results elucidate the LANA DNA binding domain structure and reveal a unique charged region that exerts a critical role in viral latent infection, likely acting through a host cell protein(s).

Organizational Affiliation

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.

Macromolecule Content

Total Structure Weight: 32.63 kDa
Atom Count: 2,027
Modeled Residue Count: 240
Deposited Residue Count: 282
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LATENCY-ASSOCIATED NUCLEAR ANTIGEN	A, B	141	Murid gammaherpesvirus 4	Mutation(s): 0
UniProt
Find proteins for O41974 (Murid herpesvirus 4) Explore O41974 Go to UniProtKB: O41974
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O41974
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.203 (Depositor), 0.212 (DCC)
R-Value Work: 0.171 (Depositor), 0.181 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.575	α = 90
b = 61.68	β = 99.36
c = 63.678	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2014-12-17
Changes: Data collection
Version 1.2: 2018-03-07
Changes: Advisory, Data collection, Source and taxonomy
Version 1.3: 2023-12-20
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description