9KBJ | pdb_00009kbj

The structure of B19V NS1_200-501/AMPPNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structural and functional studies of the main replication protein NS1 of human parvovirus B19.

Zhang, Y.Fan, B.Gao, Y.Yang, J.Zhang, W.Su, S.Li, L.Li, H.Luo, Z.Tang, G.Wang, C.Zhang, X.Liu, H.Gan, J.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf562
  • Primary Citation of Related Structures:  
    9KBG, 9KBH, 9KBI, 9KBJ

  • PubMed Abstract: 

    Parvovirus B19 (B19V) is a ubiquitous virus that can infect the majority of human population and cause erythema infectiosum, acute arthropathy, and many other diseases. The main replication protein NS1 plays a critical role in cell cycle arrest, transactivation of viral and host genes, and replication and package of B19V genome. Both DNA nicking and unwinding activities are required for the in vivo function of NS1, but the underlying basis is poorly understood. Here, we report extensive structural and biochemical studies of NS1, showing that NS1 can unwind various types of DNA substrates. The cryo-electron microscopy (cryo-EM) structures reveal the detailed mechanisms for ATP binding and hydrolysis, and DNA binding and unwinding by NS1. In addition to the SF3 HD domain, the C-terminal region is also required for double-stranded DNA (dsDNA) nicking by NS1. Unexpectedly, instead of enhancing, the dsDNA nicking activity of NS1 is negatively regulated by its DNA unwinding ability, suggesting that they likely function in different stages. This study advances our understanding of the structure and function of NS1 and other parvoviral replication proteins, such as the Rep proteins of adeno-associated virus.


  • Organizational Affiliation
    • State Key Laboratory of Genetics and Development of Complex Phenotypes, Collaborative Innovation Center of Genetics and Development, Shanghai Sci-Tech Inno Center for Infection & Immunity, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 1302Human parvovirus B19Mutation(s): 0 
Gene Names: NS1
EC: 3.6.4.12
UniProt
Find proteins for J7FCE3 (Human parvovirus B19)
Explore J7FCE3 
Go to UniProtKB:  J7FCE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7FCE3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
BA [auth J]
DA [auth K]
FA [auth L]
HA [auth B]
N [auth A]
BA [auth J],
DA [auth K],
FA [auth L],
HA [auth B],
N [auth A],
P [auth C],
R [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth J]
CA [auth K]
EA [auth L]
GA [auth B]
M [auth A]
AA [auth J],
CA [auth K],
EA [auth L],
GA [auth B],
M [auth A],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
W [auth G],
Y [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1_4122:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release