[English] 日本語
Yorodumi
- EMDB-62227: The structure of B19V NS1_200-501/AMPPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62227
TitleThe structure of B19V NS1_200-501/AMPPNP
Map data
Sample
  • Complex: B19V NS1_200-501 with AMPPNP
    • Protein or peptide: Non-structural protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsHuman parvovirus B19 / NS1 / DNA BINDING PROTEIN
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
Initiator protein NS1
Similarity search - Component
Biological speciesHuman parvovirus B19
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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

-
Structure visualization

Supplemental images

emd_62227.png

Downloads & links

-
Map

FileDownload / File: emd_62227.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 270 pix.
= 297. Å		1.1 Å/pix.
x 270 pix.
= 297. Å		1.1 Å/pix.
x 270 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05585295 - 0.096084334
Average (Standard dev.)0.0002466775 (±0.0030310494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_62227_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62227_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : B19V NS1_200-501 with AMPPNP

EntireName: B19V NS1_200-501 with AMPPNP
Components
  • Complex: B19V NS1_200-501 with AMPPNP
    • Protein or peptide: Non-structural protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

-
Supramolecule #1: B19V NS1_200-501 with AMPPNP

SupramoleculeName: B19V NS1_200-501 with AMPPNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Non-structural protein 1

MacromoleculeName: Non-structural protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 33.732672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AEVVPFNGKG TKASIKFQTM VNWLCENRVF TEDKWKLVDF NQYTLLSSSH SGSFQIQSAL KLAIYKATNL VPTSTFLLHA DFEQVMCIK DNKIVKLLLC QNYDPLLVGQ HVLKWIDKKC GKKNTLWFYG PPSTGKTNLA MAIAKSVPVY GMVNWNNENF P FNDVAGKS ...String:
AEVVPFNGKG TKASIKFQTM VNWLCENRVF TEDKWKLVDF NQYTLLSSSH SGSFQIQSAL KLAIYKATNL VPTSTFLLHA DFEQVMCIK DNKIVKLLLC QNYDPLLVGQ HVLKWIDKKC GKKNTLWFYG PPSTGKTNLA MAIAKSVPVY GMVNWNNENF P FNDVAGKS LVVWDEGIIK STIVEAAKAI LGGQPTRVDQ KMRGSVAVPG VPVVITSNGD ITFVVSGNTT TTVHAKALKE RM VKLNFTV RCSPDMGLLT EADVQQWLTW CNAQSWDHYE NWAINYTFDF PGINADALHP DLQTT

UniProtKB: Initiator protein NS1

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 11 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 11 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Cs: 0.01 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204488
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more