[English] 日本語
Yorodumi
- EMDB-46607: Infectious B19V capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46607
TitleInfectious B19V capsid
Map dataDeepEMhancer sharpened map of the serpinA3 bound to B19V capsid.
Sample
  • Complex: Human parvovirus B19 with Serpin A3
    • Complex: Serpin A3
      • Protein or peptide: Alpha-1-antichymotrypsin
    • Virus: Human parvovirus B19
KeywordsB19 / Virion / Capsid / PROTEIN BINDING
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / collagen-containing extracellular matrix / secretory granule lumen / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / collagen-containing extracellular matrix / secretory granule lumen / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human) / Human parvovirus B19
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLee H / Hafenstein S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Infectious parvovirus B19 circulates in the blood coated with active host protease inhibitors.
Authors: Hyunwook Lee / Ruben Assaraf / Suriyasri Subramanian / Dan Goetschius / Jan Bieri / Nadia M DiNunno / Remo Leisi / Carol M Bator / Susan L Hafenstein / Carlos Ros /
Abstract: The lack of a permissive cell culture system has limited high-resolution structures of parvovirus B19 (B19V) to virus-like particles (VLPs). In this study, we present the atomic resolution structure ...The lack of a permissive cell culture system has limited high-resolution structures of parvovirus B19 (B19V) to virus-like particles (VLPs). In this study, we present the atomic resolution structure (2.2 Å) of authentic B19V purified from a patient blood sample. There are significant differences compared to non-infectious VLPs. Most strikingly, two host protease inhibitors (PIs), inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) and serpinA3, were identified in complex with the capsids in all patient samples tested. The ITIH4 binds specifically to the icosahedral fivefold axis and serpinA3 occupies the twofold axis. The protein-coated virions remain infectious, and the capsid-associated PIs retain activity; however, upon virion interaction with target cells, the PIs dissociate from the capsid prior to viral entry. Our finding of an infectious virion shielded by bound host serum proteins suggests an evolutionarily favored phenomenon to evade immune surveillance and escape host protease activity.
History
DepositionAug 16, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46607.png

Downloads & links

-
Map

FileDownload / File: emd_46607.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map of the serpinA3 bound to B19V capsid.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.029534679 - 2.2661166
Average (Standard dev.)0.0006687996 (±0.021547662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map-1 of the serpinA3 bound to B19V capsid.

Fileemd_46607_half_map_1.map
AnnotationHalf map-1 of the serpinA3 bound to B19V capsid.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map-2 of the serpinA3 bound to B19V capsid.

Fileemd_46607_half_map_2.map
AnnotationHalf map-2 of the serpinA3 bound to B19V capsid.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human parvovirus B19 with Serpin A3

EntireName: Human parvovirus B19 with Serpin A3
Components
  • Complex: Human parvovirus B19 with Serpin A3
    • Complex: Serpin A3
      • Protein or peptide: Alpha-1-antichymotrypsin
    • Virus: Human parvovirus B19

-
Supramolecule #1: Human parvovirus B19 with Serpin A3

SupramoleculeName: Human parvovirus B19 with Serpin A3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #3: Serpin A3

SupramoleculeName: Serpin A3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: Human parvovirus B19

SupramoleculeName: Human parvovirus B19 / type: virus / ID: 2 / Parent: 1 / NCBI-ID: 10798 / Sci species name: Human parvovirus B19 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Alpha-1-antichymotrypsin

MacromoleculeName: Alpha-1-antichymotrypsin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.701668 KDa
SequenceString: MERMLPLLAL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL YKQLVLKAPD KNVIFSPLSI STALAFLSL GAHNTTLTEI LKGLKFNLTE TSEAEIHQSF QHLLRTLNQS SDELQLSMGN AMFVKEQLSL LDRFTEDAKR L YGSEAFAT ...String:
MERMLPLLAL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL YKQLVLKAPD KNVIFSPLSI STALAFLSL GAHNTTLTEI LKGLKFNLTE TSEAEIHQSF QHLLRTLNQS SDELQLSMGN AMFVKEQLSL LDRFTEDAKR L YGSEAFAT DFQDSAAAKK LINDYVKNGT RGKITDLIKD LDSQTMMVLV NYIFFKAKWE MPFDPQDTHQ SRFYLSKKKW VM VPMMSLH HLTIPYFRDE ELSCTVVELK YTGNASALFI LPDQDKMEEV EAMLLPETLK RWRDSLEFRE IGELYLPKFS ISR DYNLND ILLQLGIEEA FTSKADLSGI TGARNLAVSQ VVHKAVLDVF EEGTEASAAT AVKITLLSAL VETRTIVRFN RPFL MIIVP TDTQNIFFMS KVTNPKQA

UniProtKB: Alpha-1-antichymotrypsin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380278
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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