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- EMDB-23108: Human Bocavirus 1 (pH 2.6) -

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Basic information

Entry
Database: EMDB / ID: EMD-23108
TitleHuman Bocavirus 1 (pH 2.6)
Map data
Sample
  • Virus: Human bocavirus 1
    • Protein or peptide: VP2
KeywordsIcosahedral Capsid / Human Bocavirus 1 / HBoV1 / VIRUS / Parvovirus
Function / homologyParvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP2
Function and homology information
Biological speciesPrimate bocaparvovirus 1 (strain Human bocavirus 1 type 1) / Human bocavirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsLuo M / Mietzsch M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J Virol / Year: 2021
Title: pH-Induced Conformational Changes of Human Bocavirus Capsids.
Authors: Mengxiao Luo / Mario Mietzsch / Paul Chipman / Kangkang Song / Chen Xu / John Spear / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / Mavis Agbandje-McKenna /
Abstract: Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and ...Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and image reconstruction, the HBoV2 capsid structure was determined to 2.7 Å resolution at pH 7.4 and compared to the previously determined HBoV1, HBoV3, and HBoV4 structures. Consistent with previous findings, surface variable region (VR) III of the capsid protein VP3, proposed as a host tissue-tropism determinant, was structurally similar among the gastrointestinal strains HBoV2-4, but differed from HBoV1 with its tropism for the respiratory tract. Towards understanding the entry and trafficking properties of these viruses, HBoV1 and HBoV2 were further analyzed as species representatives of the two HBoV tropisms. Their cell surface glycan-binding characteristics were analyzed, and capsid structures determined to 2.5-2.7 Å resolution at pH 5.5 and 2.6, conditions normally encountered during infection. The data showed that glycans with terminal sialic acid, galactose, GlcNAc or heparan sulfate moieties do not facilitate HBoV1 or HBoV2 cellular attachment. With respect to trafficking, conformational changes common to both viruses were observed at low pH conditions localized to the VP N-terminus under the 5-fold channel, in the surface loops VR-I and VR-V and specific side-chain residues such as cysteines and histidines. The 5-fold conformational movements provide insight into the potential mechanism of VP N-terminal dynamics during HBoV infection and side-chain modifications highlight pH-sensitive regions of the capsid. Human bocaviruses (HBoVs) are associated with disease in humans. However, the lack of an animal model and a versatile cell culture system to study their life cycle limits the ability to develop specific treatments or vaccines. This study presents the structure of HBoV2, at 2.7 Å resolution, determined for comparison to the existing HBoV1, HBoV3, and HBoV4 structures, to enable the molecular characterization of strain and genus-specific capsid features contributing to tissue tropism and antigenicity. Furthermore, HBoV1 and HBoV2 structures determined under acidic conditions provide insight into capsid changes associated with endosomal and gastrointestinal acidification. Structural rearrangements of the capsid VP N-terminus, at the base of the 5-fold channel, demonstrate a disordering of a "basket" motif as pH decreases. These observations begin to unravel the molecular mechanism of HBoV infection and provide information for control strategies.
History
DepositionDec 13, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l0y
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7l0y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23108.png

Downloads & links

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Map

FileDownload / File: emd_23108.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.9 Å/pix.
x 450 pix.
= 404.55 Å		0.9 Å/pix.
x 450 pix.
= 404.55 Å		0.9 Å/pix.
x 450 pix.
= 404.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.899 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 2.5
Minimum - Maximum-11.865470999999999 - 21.110026999999999
Average (Standard dev.)0.000000004982512 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-225-225-225
Dimensions450450450
Spacing450450450
CellA=B=C: 404.55 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8990.8990.899
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z404.550404.550404.550
α/β/γ90.00090.00090.000
start NX/NY/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S213
start NC/NR/NS-225-225-225
NC/NR/NS450450450
D min/max/mean-11.86521.1100.000

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Supplemental data

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Sample components

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Entire : Human bocavirus 1

EntireName: Human bocavirus 1
Components
  • Virus: Human bocavirus 1
    • Protein or peptide: VP2

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Supramolecule #1: Human bocavirus 1

SupramoleculeName: Human bocavirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 573977 / Sci species name: Human bocavirus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Primate bocaparvovirus 1 (strain Human bocavirus 1 type 1)
Strain: Human bocavirus 1 type 1
Molecular weightTheoretical: 58.165867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GTGSIGGGKG SGVGISTGGW VGGSHFSDKY VVTKNTRQFI TTIQNGHLYK TEAIETTNQS GKSQRCVTTP WTYFNFNQYS CHFSPQDWQ RLTNEYKRFR PKAMQVKIYN LQIKQILSNG ADTTYNNDLT AGVHIFCDGE HAYPNASHPW DEDVMPDLPY K TWKLFQYG ...String:
GTGSIGGGKG SGVGISTGGW VGGSHFSDKY VVTKNTRQFI TTIQNGHLYK TEAIETTNQS GKSQRCVTTP WTYFNFNQYS CHFSPQDWQ RLTNEYKRFR PKAMQVKIYN LQIKQILSNG ADTTYNNDLT AGVHIFCDGE HAYPNASHPW DEDVMPDLPY K TWKLFQYG YIPIENELAD LDGNAAGGNA TEKALLYQMP FFLLENSDHQ VLRTGESTEF TFNFDCEWVN NERAYIPPGL MF NPKVPTR RVQYIRQNGS TAASTGRIQP YSKPTSWMTG PGLLSAQRVG PQSSDTAPFM VCTNPEGTHI NTGAAGFGSG FDP PSGCLA PTNLEYKLQW YQTPEGTGNN GNIIANPSLS MLRDQLLYKG NQTTYNLVGD IWMFPNQVWD RFPITRENPI WCKK PRADK HTIMDPFDGS IAMDHPPGTI FIKMAKIPVP TASNADSYLN IYCTGQVSCE IVWEVERYAT KNWRPERRHT ALGMS LGGE SNYTPTYHVD PTGAYIQPTS YDQCMPVKTN INKVL

UniProtKB: VP2

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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: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 50342
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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