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- EMDB-62225: The structure of B19V NS1_2-570/ssDNA/AMPPNP -

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Basic information

Entry
Database: EMDB / ID: EMD-62225
TitleThe structure of B19V NS1_2-570/ssDNA/AMPPNP
Map data
Sample
  • Complex: B19V NS1_2-570 with ssDNA and AMPPNP
    • Protein or peptide: Non-structural protein 1
    • DNA: DNA (67-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsHuman parvovirus B19 / NS1 / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host apoptosis / viral DNA genome replication / helicase activity / endonuclease activity / DNA helicase / DNA replication / hydrolase activity / host cell nucleus / DNA binding ...symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host apoptosis / viral DNA genome replication / helicase activity / endonuclease activity / DNA helicase / DNA replication / hydrolase activity / 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
Initiator protein NS1
Similarity search - Component
Biological speciesHuman parvovirus B19
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGan J / Zhang Y
Funding support China, 1 items
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, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62225.png

Downloads & links

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Map

FileDownload / File: emd_62225.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 360 pix.
= 345.24 Å		0.96 Å/pix.
x 360 pix.
= 345.24 Å		0.96 Å/pix.
x 360 pix.
= 345.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.0170019 - 2.3420925
Average (Standard dev.)-0.0011779551 (±0.06951616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 345.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62225_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62225_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : B19V NS1_2-570 with ssDNA and AMPPNP

EntireName: B19V NS1_2-570 with ssDNA and AMPPNP
Components
  • Complex: B19V NS1_2-570 with ssDNA and AMPPNP
    • Protein or peptide: Non-structural protein 1
    • DNA: DNA (67-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: B19V NS1_2-570 with ssDNA and AMPPNP

SupramoleculeName: B19V NS1_2-570 with ssDNA and AMPPNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: Non-structural protein 1

MacromoleculeName: Non-structural protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 62.681031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ELFRGVLQVS SNVLDCANDN WWCSLLDLDT SDWEPLTHTN RLMAIYLSSV ASKLDFTGGP LAGCLYFFQV ECNKFEEGYH IHVVIGGPG LNPRNLTVCV EGLFNNVLYH LVTGNVKLKF LPGMTTKGKY FRDGEQFIEN YLMKKIPLNV VWCVTNIDGY I DTCISATF ...String:
ELFRGVLQVS SNVLDCANDN WWCSLLDLDT SDWEPLTHTN RLMAIYLSSV ASKLDFTGGP LAGCLYFFQV ECNKFEEGYH IHVVIGGPG LNPRNLTVCV EGLFNNVLYH LVTGNVKLKF LPGMTTKGKY FRDGEQFIEN YLMKKIPLNV VWCVTNIDGY I DTCISATF RRGACHAKKP RMTTAINDTS SDAGEPSGTG AEVVPFNGKG TKASIKFQTM VNWLCENRVF TEDKWKLVDF NQ YTLLSSS HSGSFQIQSA LKLAIYKATN LVPTSTFLLH ADFEQVMCIK DNKIVKLLLC QNYDPLLVGQ HVLKWIDKKC GKK NTLWFY GPPSTGKTNL AMAIAKSVPV YGMVNWNNEN FPFNDVAGKS LVVWDEGIIK STIVEAAKAI LGGQPTRVDQ KMRG SVAVP GVPVVITSNG DITFVVSGNT TTTVHAKALK ERMVKLNFTV RCSPDMGLLT EADVQQWLTW CNAQSWDHYE NWAIN YTFD FPGINADALH PDLQTTPIVT DTSISSSGGE SSEELSESSF FNLITPGACN TETPRSSTPI PGTSSGESLV GSPVSS EVV AASWEE

UniProtKB: Initiator protein NS1

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Macromolecule #2: DNA (67-MER)

MacromoleculeName: DNA (67-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 20.606125 KDa
SequenceString: (DT)(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DA) (DG)(DT)(DC)(DC)(DC)(DG)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DG) (DA)(DC)(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DA) (DT) (DC)(DT)(DG)(DA)(DT)(DT) ...String:
(DT)(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DA) (DG)(DT)(DC)(DC)(DC)(DG)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DG) (DA)(DC)(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DA) (DT) (DC)(DT)(DG)(DA)(DT)(DT)(DT)(DG) (DG)(DT)(DG)(DT)(DC)(DT)(DT)(DC)(DT)(DT) (DT)(DT) (DA)(DA)(DA)(DT)(DT)(DT)(DT)

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 6 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25268
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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