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- EMDB-45191: Infectious B19V capsid -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45191
TitleInfectious B19V capsid
Map dataSubvolume of B19V capsid
Sample
  • Complex: Human parvovirus B19 with inter-alpha-trypsin inhibitor heavy chain H4
    • Complex: Inter-alpha-trypsin inhibitor heavy chain H4
      • Protein or peptide: Inter-alpha-trypsin inhibitor heavy chain H4
    • Virus: Human parvovirus B19
KeywordsB19 / Virion / Capsid / PROTEIN BINDING
Function / homology
Function and homology information


hyaluronan metabolic process / platelet dense granule lumen / endopeptidase inhibitor activity / response to cytokine / acute-phase response / serine-type endopeptidase inhibitor activity / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / extracellular exosome ...hyaluronan metabolic process / platelet dense granule lumen / endopeptidase inhibitor activity / response to cytokine / acute-phase response / serine-type endopeptidase inhibitor activity / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Inter-alpha-trypsin inhibitor heavy chain, C-terminal / : / Inter-alpha-trypsin inhibitor heavy chain C-terminus / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Inter-alpha-trypsin inhibitor heavy chain, C-terminal / : / Inter-alpha-trypsin inhibitor heavy chain C-terminus / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Inter-alpha-trypsin inhibitor heavy chain H4
Similarity search - Component
Biological speciesHomo sapiens (human) / Human parvovirus B19
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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
DepositionJun 4, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45191.png

Downloads & links

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Map

FileDownload / File: emd_45191.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubvolume of B19V capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 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: 0.336
Minimum - Maximum-1.0774088 - 1.9321834
Average (Standard dev.)0.011595581 (±0.0857969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map-2 of the subvolume of B19V capsid

Fileemd_45191_half_map_1.map
AnnotationHalf map-2 of the subvolume of B19V capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map-1 of the subvolume of B19V capsid

Fileemd_45191_half_map_2.map
AnnotationHalf map-1 of the subvolume of B19V capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human parvovirus B19 with inter-alpha-trypsin inhibitor heavy chain H4

EntireName: Human parvovirus B19 with inter-alpha-trypsin inhibitor heavy chain H4
Components
  • Complex: Human parvovirus B19 with inter-alpha-trypsin inhibitor heavy chain H4
    • Complex: Inter-alpha-trypsin inhibitor heavy chain H4
      • Protein or peptide: Inter-alpha-trypsin inhibitor heavy chain H4
    • Virus: Human parvovirus B19

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Supramolecule #1: Human parvovirus B19 with inter-alpha-trypsin inhibitor heavy chain H4

SupramoleculeName: Human parvovirus B19 with inter-alpha-trypsin inhibitor heavy chain H4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #3: Inter-alpha-trypsin inhibitor heavy chain H4

SupramoleculeName: Inter-alpha-trypsin inhibitor heavy chain H4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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

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Macromolecule #1: Inter-alpha-trypsin inhibitor heavy chain H4

MacromoleculeName: Inter-alpha-trypsin inhibitor heavy chain H4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.47025 KDa
SequenceString: MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR ANTVQEATFQ MELPKKAFIT NFSMIIDGM TYPGIIKEKA EAQAQYSAAV AKGKSAGLVK ATGRNMEQFQ VSVSVAPNAK ITFELVYEEL LKRRLGVYEL L LKVRPQQL ...String:
MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR ANTVQEATFQ MELPKKAFIT NFSMIIDGM TYPGIIKEKA EAQAQYSAAV AKGKSAGLVK ATGRNMEQFQ VSVSVAPNAK ITFELVYEEL LKRRLGVYEL L LKVRPQQL VKHLQMDIHI FEPQGISFLE TESTFMTNQL VDALTTWQNK TKAHIRFKPT LSQQQKSPEQ QETVLDGNLI IR YDVDRAI SGGSIQIENG YFVHYFAPEG LTTMPKNVVF VIDKSGSMSG RKIQQTREAL IKILDDLSPR DQFNLIVFST EAT QWRPSL VPASAENVNK ARSFAAGIQA LGGTNINDAM LMAVQLLDSS NQEERLPEGS VSLIILLTDG DPTVGETNPR SIQN NVREA VSGRYSLFCL GFGFDVSYAF LEKLALDNGG LARRIHEDSD SALQLQDFYQ EVANPLLTAV TFEYPSNAVE EVTQN NFRL LFKGSEMVVA GKLQDRGPDV LTATVSGKLP TQNITFQTES SVAEQEAEFQ SPKYIFHNFM ERLWAYLTIQ QLLEQT VSA SDADQQALRN QALNLSLAYS FVTPLTSMVV TKPDDQEQSQ VAEKPMEGES RNRNVHSGST FFKYYLQGAK IPKPEAS FS PRRGWNRQAG AAGSRMNFRP GVLSSRQLGL PGPPDVPDHA AYHPFRRLAI LPASAPPATS NPDPAVSRVM NMKIEETT M TTQTPAPIQA PSAILPLPGQ SVERLCVDPR HRQGPVNLLS DPEQGVEVTG QYEREKAGFS WIEVTFKNPL VWVHASPEH VVVTRNRRSS AYKWKETLFS VMPGLKMTMD KTGLLLLSDP DKVTIGLLFW DGRGEGLRLL LRDTDRFSSH VGGTLGQFYQ EVLWGSPAA SDDGRRTLRV QGNDHSATRE RRLDYQEGPP GVEISCWSVE L

UniProtKB: Inter-alpha-trypsin inhibitor heavy chain H4

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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) / 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68391
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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