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- EMDB-45958: Bufavirus 1 at pH 4.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-45958
TitleBufavirus 1 at pH 4.0
Map dataBufavirus 1 at pH 4.0
Sample
  • Virus: Bufavirus-1
    • Protein or peptide: VP1
KeywordsBufavirus / parvovirus / VIRUS LIKE PARTICLE
Function / homologyPhospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP1
Function and homology information
Biological speciesBufavirus-1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGulkis MC / McKenna R / Bennett AD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2024
Title: Structural Characterization of Human Bufavirus 1: Receptor Binding and Endosomal pH-Induced Changes.
Authors: Mitchell Gulkis / Mengxiao Luo / Paul Chipman / Mario Mietzsch / Maria Söderlund-Venermo / Antonette Bennett / Robert McKenna /
Abstract: Bufaviruses (BuV) are members of the of the genus. They are non-enveloped, T = 1 icosahedral ssDNA viruses isolated from patients exhibiting acute diarrhea. The lack of treatment options and a ...Bufaviruses (BuV) are members of the of the genus. They are non-enveloped, T = 1 icosahedral ssDNA viruses isolated from patients exhibiting acute diarrhea. The lack of treatment options and a limited understanding of their disease mechanisms require studying these viruses on a molecular and structural level. In the present study, we utilize glycan arrays and cell binding assays to demonstrate that BuV1 capsid binds terminal sialic acid (SIA) glycans. Furthermore, using cryo-electron microscopy (cryo-EM), SIA is shown to bind on the 2/5-fold wall of the capsid surface. Interestingly, the capsid residues stabilizing SIA binding are conserved in all human BuVs identified to date. Additionally, biophysical assays illustrate BuV1 capsid stabilization during endo-lysosomal (pH 7.4-pH 4) trafficking and capsid destabilization at pH 3 and less, which correspond to the pH of the stomach. Hence, we determined the cryo-EM structures of BuV1 capsids at pH 7.4, 4.0, and 2.6 to 2.8 Å, 3.2 Å, and 2.7 Å, respectively. These structures reveal capsid structural rearrangements during endo-lysosomal escape and provide a potential mechanism for this process. The structural insights gained from this study will add to the general knowledge of human pathogenic parvoviruses. Furthermore, the identification of the conserved SIA receptor binding site among BuVs provides a possible targetable surface-accessible pocket for the design of small molecules to be developed as anti-virals for these viruses.
History
DepositionJul 28, 2024-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45958.png

Downloads & links

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Map

FileDownload / File: emd_45958.map.gz / Format: CCP4 / Size: 396.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBufavirus 1 at pH 4.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.05 Å/pix.
x 470 pix.
= 493.97 Å		1.05 Å/pix.
x 470 pix.
= 493.97 Å		1.05 Å/pix.
x 470 pix.
= 493.97 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.051 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-12.6959 - 25.348500000000001
Average (Standard dev.)0.000000000845804 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-235-235-235
Dimensions470470470
Spacing470470470
CellA=B=C: 493.97 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_45958_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_45958_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bufavirus-1

EntireName: Bufavirus-1
Components
  • Virus: Bufavirus-1
    • Protein or peptide: VP1

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Supramolecule #1: Bufavirus-1

SupramoleculeName: Bufavirus-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1209382 / Sci species name: Bufavirus-1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4 MDa
Virus shellShell ID: 1 / Diameter: 260.0 Å / T number (triangulation number): 1

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Bufavirus-1
Molecular weightTheoretical: 80.543203 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPAIRKARGW VPPGYNYLGP FNQDFNKKPT NPSDNAARKH DLEYNKLIKQ GHNPYWNYNH ADEDFIKETD QATDWGGKFG NFVFRAKRA LAPELAPPAK KKTKTKHTEP EYSHKHIKAG TKRGKPFYLF VNLARKKARM TDTQDVSEQQ SDQPSVASTN A KAGGGGGG ...String:
MPAIRKARGW VPPGYNYLGP FNQDFNKKPT NPSDNAARKH DLEYNKLIKQ GHNPYWNYNH ADEDFIKETD QATDWGGKFG NFVFRAKRA LAPELAPPAK KKTKTKHTEP EYSHKHIKAG TKRGKPFYLF VNLARKKARM TDTQDVSEQQ SDQPSVASTN A KAGGGGGG GGSGVGHSTG NYNNRTEFYY HGDEVTIVCH SSRHIHLNMS ESEEYKIYDT DRGPRFPTDQ TLQGRDTIND SY HAQVETP WFLINPNSWG TWMNPADFQQ LTTTCREVTL EHLDQTLDNI VIKTVSKQGS GAEETTQYNN DLTALLQVAL DKS NQLPWV ADNMYLDSLG YIPWRPCKLK QYSYHVNFWN TIDIISGPQQ NQWQQVKKEI RWDDLQFTPI ETTTEIDLLR TGDS WTSGP YKFNTKPTQL SYHWQSTRHT GSVHPTDPPN AIGQQGQNIR DINGWQWGDR SDPMSAATRV SNFHIGYSWP EWRIH YGSG GPAINPGAPF SQAPWSTDPQ VRLTQGASEK AIFDYNHGDD DPAHRDQWWQ NNLPITGQTN WAPKNAHQAN LSSNVP SRQ EFWTQDYHNT FGPFTAVDDV GIQYPWGAIW TKTPDTTHKP MMSAHAPFIC KDGPPGQLLV KLAPNYTENL QTDGLGN NR IVTYATFWWT GKLILKGKLR LPRQFNLYNL PGRPRGTEAK KFLPNEIGHF ELPFMPGRCM PNYTM

UniProtKB: VP1

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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

Concentration0.5 mg/mL
BufferpH: 4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
20.0 mMC6H13NO4SMES
20.0 mMCH3COONaSodium Acetate
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number real images: 827 / Average electron dose: 75.0 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 / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 121209
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 55060
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bwx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 174.8 / Target criteria: Cross-correlation coefficient
Output model

PDB-9cv9:
Bufavirus 1 at pH 4.0

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