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- EMDB-45184: Infectious B19V capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-45184
TitleInfectious B19V capsid
Map dataA deepEMhancer-processed map of B19V-ITIH4 complex
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
      • Protein or peptide: Capsid protein 2
KeywordsB19 / Virion / Capsid / VIRAL PROTEIN
Function / homology
Function and homology information


hyaluronan metabolic process / platelet dense granule lumen / endopeptidase inhibitor activity / T=1 icosahedral viral capsid / response to cytokine / acute-phase response / serine-type endopeptidase inhibitor activity / Platelet degranulation / : / blood microparticle ...hyaluronan metabolic process / platelet dense granule lumen / endopeptidase inhibitor activity / T=1 icosahedral viral capsid / response to cytokine / acute-phase response / serine-type endopeptidase inhibitor activity / Platelet degranulation / : / blood microparticle / structural molecule activity / 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 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 ...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 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / 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 / Capsid protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Human parvovirus B19
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45184.png

Downloads & links

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Map

FileDownload / File: emd_45184.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA deepEMhancer-processed map of B19V-ITIH4 complex
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: 0.115
Minimum - Maximum-0.104992844 - 2.1851652
Average (Standard dev.)0.004518545 (±0.050323907)
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: B-factor sharpened map of B19V-ITIH4 complex

Fileemd_45184_additional_1.map
AnnotationB-factor sharpened map of B19V-ITIH4 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map-1 of B19V-ITIH4 complex

Fileemd_45184_half_map_1.map
AnnotationA half map-1 of B19V-ITIH4 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map-1 of B19V-ITIH4 complex

Fileemd_45184_half_map_2.map
AnnotationA half map-1 of B19V-ITIH4 complex
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
      • Protein or peptide: Capsid protein 2

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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: #2
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 / Macromolecule list: #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: Capsid protein 2

MacromoleculeName: Capsid protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 60.916016 KDa
SequenceString: MTSVNSAEAS TGAGGGGSNP VKSMWSEGAT FSANSVTCTF SRQFLIPYDP EHHYKVFSPA ASSCHNASGK EAKVCTISPI MGYSTPWRY LDFNALNLFF SPLEFQHLIE NYGSIAPDAL TVTISEIAVK DVTDKTGGGV QVTDSTTGRL CMLVDHEYKY P YVLGQGQD ...String:
MTSVNSAEAS TGAGGGGSNP VKSMWSEGAT FSANSVTCTF SRQFLIPYDP EHHYKVFSPA ASSCHNASGK EAKVCTISPI MGYSTPWRY LDFNALNLFF SPLEFQHLIE NYGSIAPDAL TVTISEIAVK DVTDKTGGGV QVTDSTTGRL CMLVDHEYKY P YVLGQGQD TLAPELPIWV YFPPQYAYLT VGDVNTQGIS GDSKKLASEE SAFYVLEHSS FQLLGTGGTA TMSYKFPPVP PE NLEGCSQ HFYEMYNPLY GSRLGVPDTL GGDPKFRSLT HEDHAIQPQN FMPGPLVNSV STKEGDSSNT GAGKALTGLS TGT SQNTRI SLRPGPVSQP YHHWDTDKYV TGINAISHGQ TTYGNAEDKE YQQGVGRFPN EKEQLKQLQG LNMHTYFPNK GTQQ YTDQI ERPLMVGSVW NRRALHYESQ LWSKIPNLDD SFKTQFAALG GWGLHQPPPQ IFLKILPQSG PIGGIKSMGI TTLVQ YAVG IMTVTMTFKL GPRKATGRWN PQPGVYPPHA AGHLPYVLYD PTATDAKQHH RHGYEKPEEL WTAKSRVHPL

UniProtKB: Capsid protein 2

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Macromolecule #2: Inter-alpha-trypsin inhibitor heavy chain H4

MacromoleculeName: Inter-alpha-trypsin inhibitor heavy chain H4 / type: protein_or_peptide / ID: 2 / 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
Details: C1 reconstruction was performed by using ISECC with selected particles from subparticle analysis
Number images used: 192181
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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