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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7302 | |||||||||
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Title | Atomic resolution structure of human bufavirus 3 | |||||||||
![]() | Atomic resolution structure of human bufavirus 3 | |||||||||
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![]() | parvovirus / protoparvovirus / Bufavirus / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Parvovirus 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
![]() | Mietzsch M / Agbandje-McKenna M | |||||||||
![]() | ![]() Title: Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy. Authors: Maria Ilyas / Mario Mietzsch / Shweta Kailasan / Elina Väisänen / Mengxiao Luo / Paul Chipman / J Kennon Smith / Justin Kurian / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / ...Authors: Maria Ilyas / Mario Mietzsch / Shweta Kailasan / Elina Väisänen / Mengxiao Luo / Paul Chipman / J Kennon Smith / Justin Kurian / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / Mavis Agbandje-McKenna / ![]() ![]() Abstract: Bufavirus strain 1 (BuV1), a member of the genus of the , was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated ...Bufavirus strain 1 (BuV1), a member of the genus of the , was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65-73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI), α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 63 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.6 KB 11.6 KB | Display Display | ![]() |
Images | ![]() | 330.6 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 551.3 KB | Display | ![]() |
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Full document | ![]() | 550.9 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bx1MC ![]() 7300C ![]() 7301C ![]() 6bwxC ![]() 6bx0C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Atomic resolution structure of human bufavirus 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Bufavirus-3
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Bufavirus-3
Supramolecule | Name: Bufavirus-3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1391667 / Sci species name: Bufavirus-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4 MDa |
Virus shell | Shell ID: 1 / Name: BuV3 capsid |
-Macromolecule #1: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 61.565652 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SGVGHSTGNY NNRTIFHYHG DEVTIICHAT RHIHLNMSPT EEYKIYDTNH GPEFPNTGDQ TQQGRNTVND SYHAKVETPW YLINPNSWG IWFNPADFQQ LITTCTHVTI ETLTQEIDNI VIKTVSKQGS GAEETTQYNN DLTALLEVAL DKSNMLPWVA D NMYLNSLG ...String: SGVGHSTGNY NNRTIFHYHG DEVTIICHAT RHIHLNMSPT EEYKIYDTNH GPEFPNTGDQ TQQGRNTVND SYHAKVETPW YLINPNSWG IWFNPADFQQ LITTCTHVTI ETLTQEIDNI VIKTVSKQGS GAEETTQYNN DLTALLEVAL DKSNMLPWVA D NMYLNSLG YIPWRPCKLT QFCYHTNFYN TINLLEGTQQ NQWSQIKEGI QYDNLQFTPI ETSAEIDLLR TGDSWTSGTY HF KCKPTQL FYHWQSTRHI GAPHPTTSPE QEGQKGQIIQ DTNGWQWGDR DNPISASTTV KDFHIGYSWP EWRWHYSTGG PSI NPGSAF SQTPWGSEVG GTRLTQGASE KAIFDYNHGE AEPGHRDQWW QNNAQQTGQT NWAIKNAHQS ELRNATASRE TFWT QDYHN TFGPYTAVDD VGIQYPWGAM WGKQPDTTHK PMMSAHAPFT CQNGPPGQLL VKLAPNYTDS LNNEGLQTNR IVTFA TFWW TGRCTFKAKL RTPRQFNAYQ LPGIPSGTNP KKFVPDAIGR FELPFMPGRA MPNYTY UniProtKB: VP2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 2-20 / Number real images: 689 / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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Output model | ![]() PDB-6bx1: |