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- EMDB-45160: Infectious B19V capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-45160
TitleInfectious B19V capsid
Map dataA sharpened map of B19V-serpinA3 asymmetric complex map
Sample
  • Complex: Complex of B19V-ITIH4-serpinA3
    • Complex: Capsid protein 2
      • Protein or peptide: Capsid protein 2
    • Complex: ITIH4-serpinA3
      • Protein or peptide: Alpha-1-antichymotrypsin His-Pro-less
KeywordsB19 / Virion / Capsid / VIRAL PROTEIN
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 / extracellular space / DNA binding / 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 VP1/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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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
DepositionMay 31, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45160.png

Downloads & links

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Map

FileDownload / File: emd_45160.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA sharpened map of B19V-serpinA3 asymmetric complex map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 512 pix.
= 552.96 Å		1.08 Å/pix.
x 512 pix.
= 552.96 Å		1.08 Å/pix.
x 512 pix.
= 552.96 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: 0.05
Minimum - Maximum-0.16213317 - 0.25574148
Average (Standard dev.)0.00015770542 (±0.01254842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 552.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The deepEMhancer sharpened map of the B19V-serpinA3 asymmetric...

Fileemd_45160_additional_1.map
AnnotationThe deepEMhancer sharpened map of the B19V-serpinA3 asymmetric complex map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half-map #2 of the B19V-serpinA3 asymmetric complex map

Fileemd_45160_half_map_1.map
AnnotationThe half-map #2 of the B19V-serpinA3 asymmetric complex map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half-map #1 of the B19V-serpinA3 asymmetric complex map

Fileemd_45160_half_map_2.map
AnnotationThe half-map #1 of the B19V-serpinA3 asymmetric complex map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of B19V-ITIH4-serpinA3

EntireName: Complex of B19V-ITIH4-serpinA3
Components
  • Complex: Complex of B19V-ITIH4-serpinA3
    • Complex: Capsid protein 2
      • Protein or peptide: Capsid protein 2
    • Complex: ITIH4-serpinA3
      • Protein or peptide: Alpha-1-antichymotrypsin His-Pro-less

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Supramolecule #1: Complex of B19V-ITIH4-serpinA3

SupramoleculeName: Complex of B19V-ITIH4-serpinA3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Capsid protein 2

SupramoleculeName: Capsid protein 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human parvovirus B19

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Supramolecule #3: ITIH4-serpinA3

SupramoleculeName: ITIH4-serpinA3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein 2

MacromoleculeName: Capsid protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 60.78482 KDa
SequenceString: TSVNSAEAST GAGGGGSNPV KSMWSEGATF SANSVTCTFS RQFLIPYDPE HHYKVFSPAA SSCHNASGKE AKVCTISPIM GYSTPWRYL DFNALNLFFS PLEFQHLIEN YGSIAPDALT VTISEIAVKD VTDKTGGGVQ VTDSTTGRLC MLVDHEYKYP Y VLGQGQDT ...String:
TSVNSAEAST GAGGGGSNPV KSMWSEGATF SANSVTCTFS RQFLIPYDPE HHYKVFSPAA SSCHNASGKE AKVCTISPIM GYSTPWRYL DFNALNLFFS PLEFQHLIEN YGSIAPDALT VTISEIAVKD VTDKTGGGVQ VTDSTTGRLC MLVDHEYKYP Y VLGQGQDT LAPELPIWVY FPPQYAYLTV GDVNTQGISG DSKKLASEES AFYVLEHSSF QLLGTGGTAT MSYKFPPVPP EN LEGCSQH FYEMYNPLYG SRLGVPDTLG GDPKFRSLTH EDHAIQPQNF MPGPLVNSVS TKEGDSSNTG AGKALTGLST GTS QNTRIS LRPGPVSQPY HHWDTDKYVT GINAISHGQT TYGNAEDKEY QQGVGRFPNE KEQLKQLQGL NMHTYFPNKG TQQY TDQIE RPLMVGSVWN RRALHYESQL WSKIPNLDDS FKTQFAALGG WGLHQPPPQI FLKILPQSGP IGGIKSMGIT TLVQY AVGI MTVTMTFKLG PRKATGRWNP QPGVYPPHAA GHLPYVLYDP TATDAKQHHR HGYEKPEELW TAKSRVHPL

UniProtKB: Capsid protein 2

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Macromolecule #2: Alpha-1-antichymotrypsin His-Pro-less

MacromoleculeName: Alpha-1-antichymotrypsin His-Pro-less / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.50075 KDa
SequenceString: GLASANVDFA FSLYKQLVLK APDKNVIFSP LSISTALAFL SLGAHNTTLT EILKGLKFNL TETSEAEIHQ SFQHLLRTLN QSSDELQLS MGNAMFVKEQ LSLLDRFTED AKRLYGSEAF ATDFQDSAAA KKLINDYVKN GTRGKITDLI KDLDSQTMMV L VNYIFFKA ...String:
GLASANVDFA FSLYKQLVLK APDKNVIFSP LSISTALAFL SLGAHNTTLT EILKGLKFNL TETSEAEIHQ SFQHLLRTLN QSSDELQLS MGNAMFVKEQ LSLLDRFTED AKRLYGSEAF ATDFQDSAAA KKLINDYVKN GTRGKITDLI KDLDSQTMMV L VNYIFFKA KWEMPFDPQD THQSRFYLSK KKWVMVPMMS LHHLTIPYFR DEELSCTVVE LKYTGNASAL FILPDQDKME EV EAMLLPE TLKRWRDSLE FREIGELYLP KFSISRDYNL NDILLQLGIE EAFTSKADLS GITGARNLAV SQVVHKAVLD VFE EGTEAS AATAVKITLL SALVETRTIV RFNRPFLMII VPTDTQNIFF MSKVTNPKQ

UniProtKB: Alpha-1-antichymotrypsin

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380278
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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