4K2J | pdb_00004k2j

Decameric ring structure of KSHV (HHV-8) latency-associated nuclear antigen (LANA) DNA binding domain

PDB DOI: https://doi.org/10.2210/pdb4K2J/pdb

Classification: DNA BINDING PROTEIN, viral protein
Organism(s): Human gammaherpesvirus 8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-09 Released: 2013-11-06
Deposition Author(s): Domsic, J.F., Marmorstein, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular Basis for Oligomeric-DNA Binding and Episome Maintenance by KSHV LANA.

Domsic, J.F., Chen, H.S., Lu, F., Marmorstein, R., Lieberman, P.M.

(2013) PLoS Pathog 9: e1003672-e1003672

PubMed: 24146617 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1003672
Primary Citation Related Structures:
4K2J

PubMed Abstract:
LANA is the KSHV-encoded terminal repeat binding protein essential for viral replication and episome maintenance during latency. We have determined the X-ray crystal structure of LANA C-terminal DNA binding domain (LANADBD) to reveal its capacity to form a decameric ring with an exterior DNA binding surface. The dimeric core is structurally similar to EBV EBNA1 with an N-terminal arm that regulates DNA binding and is required for replication function. The oligomeric interface between LANA dimers is dispensable for single site DNA binding, but is required for cooperative DNA binding, replication function, and episome maintenance. We also identify a basic patch opposite of the DNA binding surface that is responsible for the interaction with BRD proteins and contributes to episome maintenance function. The structural features of LANADBD suggest a novel mechanism of episome maintenance through DNA-binding induced oligomeric assembly.

Organizational Affiliation

Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, United States of America.

Macromolecule Content

Total Structure Weight: 160.61 kDa
Atom Count: 11,548
Modeled Residue Count: 1,364
Deposited Residue Count: 1,400
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KSHV (HHV-8) latency-associated nuclear antigen (LANA)	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	140	Human gammaherpesvirus 8	Mutation(s): 0 Gene Names: ORF73
UniProt
Find proteins for Q9DUN0 (Human herpesvirus 8) Explore Q9DUN0 Go to UniProtKB: Q9DUN0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9DUN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain OA [auth J] SDF format, chain NA [auth J] SDF format, chain K [auth A] SDF format, chain IA [auth I] SDF format, chain DA [auth G] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain OA [auth J] MOL2 format, chain NA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth I] MOL2 format, chain DA [auth G] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain OA [auth J] mmCIF format, chain NA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth I] mmCIF format, chain DA [auth G]	DA [auth G] IA [auth I] K [auth A] NA [auth J] OA [auth J] DA [auth G], IA [auth I], K [auth A], NA [auth J], OA [auth J], P [auth C], Q [auth C], U [auth E], V [auth E]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Focus chain IA [auth I] Focus chain K [auth A] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth E] Focus chain V [auth E] Interactions & Density Focus chain DA [auth G] Focus chain IA [auth I] Focus chain K [auth A] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth E] Focus chain V [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain PA [auth J] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain MA [auth I] SDF format, chain M [auth A] SDF format, chain LA [auth I] SDF format, chain L [auth A] SDF format, chain KA [auth I] SDF format, chain JA [auth I] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain FA [auth H] SDF format, chain EA [auth G] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain PA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain PA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] CA [auth F] EA [auth G] FA [auth H] AA [auth F], BA [auth F], CA [auth F], EA [auth G], FA [auth H], GA [auth H], HA [auth H], JA [auth I], KA [auth I], L [auth A], LA [auth I], M [auth A], MA [auth I], N [auth B], O [auth B], PA [auth J], R [auth C], S [auth C], T [auth D], W [auth E], X [auth E], Y [auth E], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth B] Focus chain O [auth B] Focus chain PA [auth J] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth B] Focus chain O [auth B] Focus chain PA [auth J] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]