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- PDB-9kbh: The structure of B19V NS1_2-570/ssDNA/AMPPNP -

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Basic information

Entry
Database: PDB / ID: 9kbh
TitleThe structure of B19V NS1_2-570/ssDNA/AMPPNP
Components
  • DNA (67-MER)
  • Non-structural protein 1
KeywordsDNA BINDING PROTEIN/DNA / Human parvovirus B19 / NS1 / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


viral genome replication / endonuclease activity / DNA helicase / DNA replication / host cell nucleus / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Rep protein catalytic-like / Rep protein catalytic domain like / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Initiator protein NS1
Similarity search - Component
Biological speciesHuman parvovirus B19
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGan, J. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural and functional studies of the main replication protein NS1 of human parvovirus B19.
Authors: Yixi Zhang / Boming Fan / Yanqing Gao / Jie Yang / Weizhen Zhang / Shichen Su / Linxi Li / Huili Li / Zhaorong Luo / Guangli Tang / Chenxi Wang / Xueting Zhang / Hehua Liu / Jianhua Gan /
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 ...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.
History
DepositionOct 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
C: Non-structural protein 1
D: Non-structural protein 1
E: Non-structural protein 1
F: Non-structural protein 1
H: DNA (67-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,82717
Polymers396,6927
Non-polymers3,13410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Non-structural protein 1


Mass: 62681.031 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parvovirus B19 / Production host: Escherichia coli (E. coli) / References: UniProt: I7BP20
#2: DNA chain DNA (67-MER)


Mass: 20606.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human parvovirus B19
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: B19V NS1_2-570 with ssDNA and AMPPNP / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.38 MDa / Experimental value: YES
Source (natural)Organism: Human parvovirus B19
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.1_4122: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25268 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314121
ELECTRON MICROSCOPYf_angle_d0.50319302
ELECTRON MICROSCOPYf_dihedral_angle_d9.3981904
ELECTRON MICROSCOPYf_chiral_restr0.042223
ELECTRON MICROSCOPYf_plane_restr0.0042359

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