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- PDB-9c2t: Infectious B19V capsid -

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Basic information

Entry
Database: PDB / ID: 9c2t
TitleInfectious B19V capsid
Components
  • Alpha-1-antichymotrypsin His-Pro-less
  • Capsid protein 2
KeywordsVIRAL PROTEIN / B19 / Virion / Capsid
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / T=1 icosahedral viral capsid / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : ...maintenance of gastrointestinal epithelium / T=1 icosahedral viral capsid / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : / secretory granule lumen / blood microparticle / inflammatory response / Neutrophil degranulation / structural molecule activity / 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 / Parvovirus coat protein VP2 ...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 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Alpha-1-antichymotrypsin / Capsid protein 2
Similarity search - Component
Biological speciesHuman parvovirus B19
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLee, H. / Hafenstein, S.
Funding support1items
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
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Nov 13, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Jun 4, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein 2
B: Capsid protein 2
C: Capsid protein 2
D: Capsid protein 2
E: Capsid protein 2
F: Capsid protein 2
S: Alpha-1-antichymotrypsin His-Pro-less


Theoretical massNumber of molelcules
Total (without water)407,2107
Polymers407,2107
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Capsid protein 2 / Capsid protein VP2 / VP2 / VP2 protein


Mass: 60784.820 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human parvovirus B19 / References: UniProt: Q784T0
#2: Protein Alpha-1-antichymotrypsin His-Pro-less / Serpin A3


Mass: 42500.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01011
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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of B19V-ITIH4-serpinA3COMPLEXall0MULTIPLE SOURCES
2Capsid protein 2COMPLEX#11NATURAL
3ITIH4-serpinA3COMPLEX#21NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Human parvovirus B1910798
33Homo sapiens (human)9606
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 100 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 380278 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327780
ELECTRON MICROSCOPYf_angle_d0.50337864
ELECTRON MICROSCOPYf_dihedral_angle_d5.4833735
ELECTRON MICROSCOPYf_chiral_restr0.044091
ELECTRON MICROSCOPYf_plane_restr0.0044926

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