Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.52 kDa 
• Atom Count: 2329 
• Residue Count: 235 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

6LMJ

ASFV pA104R in complex with double-strand DNA

• DOI: 10.2210/pdb6LMJ/pdb
• NDB: 6LMJ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): African swine fever virus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-25 Released: 2020-05-13 
• Deposition Author(s): Wang, H., Qi, J., Chai, Y., Gao, F., Liu, R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.256 
• R-Value Observed: 0.257 

Literature

The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives.

Liu, R., Sun, Y., Chai, Y., Li, S., Li, S., Wang, L., Su, J., Yu, S., Yan, J., Gao, F., Zhang, G., Qiu, H.J., Gao, G.F., Qi, J., Wang, H.

(2020) Proc Natl Acad Sci U S A 117: 11000-11009

• PubMed: 32358196 
• DOI: 10.1073/pnas.1922523117
• Structures With Same Primary Citation


• PubMed Abstract: 
  

African swine fever virus (ASFV) is a highly contagious nucleocytoplasmic large DNA virus (NCLDV) that causes nearly 100% mortality in swine. The development of effective vaccines and drugs against this virus is urgently needed. pA104R, an ASFV-derived histone-like protein, shares sequence and functional similarity with bacterial HU/IHF family members and is essential for viral replication. Herein, we solved the crystal structures of pA104R in its apo state as well as in complex with DNA. Apo-pA104R forms a homodimer and folds into an architecture conserved in bacterial heat-unstable nucleoid proteins/integration host factors (HUs/IHFs). The pA104R-DNA complex structure, however, uncovers that pA104R has a DNA binding pattern distinct from its bacterial homologs, that is, the β-ribbon arms of pA104R stabilize DNA binding by contacting the major groove instead of the minor groove. Mutations of the basic residues at the base region of the β-strand DNA binding region (BDR), rather than those in the β-ribbon arms, completely abolished DNA binding, highlighting the major role of the BDR base in DNA binding. An overall DNA bending angle of 93.8° is observed in crystal packing of the pA104R-DNA complex structure, which is close to the DNA bending angle in the HU-DNA complex. Stilbene derivatives SD1 and SD4 were shown to disrupt the binding between pA104R and DNA and inhibit the replication of ASFV in primary porcine alveolar macrophages. Collectively, these results reveal the structural basis of pA104R binding to DNA highlighting the importance of the pA104R-DNA interaction in the ASFV replication cycle and provide inhibitor leads for ASFV chemotherapy.

---

Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China; [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
A104R	A, B	110	African swine fever virus	Mutation(s): 0  Gene Names: A104R, A104R CDS, BA71V-A104R, AFSV47Ss_0056, ASFV-Georgia_4-058
Find proteins for A0A0A1E0L7 (African swine fever virus) Go to UniProtKB:  A0A0A1E0L7

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*A)-3')	C, D	19	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.256 
• R-Value Observed: 0.257 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.358	α = 90
b = 89.095	β = 100.16
c = 53.227	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-12-25 
• Released Date: 2020-05-13 
Deposition Author(s): Wang, H., Qi, J., Chai, Y., Gao, F., Liu, R.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31941003
Chinese Academy of Sciences	China	KJZD-SW-L06-01
National Natural Science Foundation of China (NSFC)	China	31700149

Revision History 

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-06-03
  Changes: Database references