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- EMDB-32102: Structure of infectious bursal disease virus Gx strain -

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Basic information

Entry
Database: EMDB / ID: EMD-32102
TitleStructure of infectious bursal disease virus Gx strain
Map data
Sample
  • Virus: Infectious bursal disease virus (Gumboro virus)
    • Protein or peptide: Structural polyprotein
KeywordsIBDV / icosahedral / very virulent / VIRUS
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesAvian infectious bursal disease virus (Gumboro virus) / Infectious bursal disease virus (Gumboro virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBao KY / Zhu P
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31430087 China
National Natural Science Foundation of China (NSFC)31425007 China
CitationJournal: Sci Bull (Beijing) / Year: 2022
Title: Cryo-EM structures of infectious bursal disease viruses with different virulences provide insights into their assembly and invasion
Authors: Bao K / Qi X / Lia Y / Gong M / Wang M / Zhu P
History
DepositionOct 23, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32102.png

Downloads & links

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Map

FileDownload / File: emd_32102.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 640 pix.
= 864. Å		1.35 Å/pix.
x 640 pix.
= 864. Å		1.35 Å/pix.
x 640 pix.
= 864. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.12221756 - 0.20965677
Average (Standard dev.)0.0016275465 (±0.011953413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 864.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Infectious bursal disease virus

EntireName: Infectious bursal disease virus (Gumboro virus)
Components
  • Virus: Infectious bursal disease virus (Gumboro virus)
    • Protein or peptide: Structural polyprotein

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Supramolecule #1: Infectious bursal disease virus

SupramoleculeName: Infectious bursal disease virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10995 / Sci species name: Infectious bursal disease virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Avian infectious bursal disease virus (Gumboro virus)
Molecular weightTheoretical: 47.028871 KDa
SequenceString: MTNLQDQTQQ IVPFIRSLLM PTTGPASIPD DTLEKHTLRS ETSTYNLTVG DTGSGLIVFF PGFPGSIVGA HYTLQSNGNY KFDQMLLTA QNLPASYNYC RLVSRSLTVR SSTLPGGVYA LNGTINAVTF QGSLSELTDV SYNGLMSATA NINDKIGNVL V GEGVTVLS ...String:
MTNLQDQTQQ IVPFIRSLLM PTTGPASIPD DTLEKHTLRS ETSTYNLTVG DTGSGLIVFF PGFPGSIVGA HYTLQSNGNY KFDQMLLTA QNLPASYNYC RLVSRSLTVR SSTLPGGVYA LNGTINAVTF QGSLSELTDV SYNGLMSATA NINDKIGNVL V GEGVTVLS LPTSYDLGYV RLGDPIPAIG LDPKMVATCD SSDRPRVYTI TAADDYQFSS QYQAGGVTIT LFSANIDAIT SL SIGGELV FQTSVQGLIL GATIYLIGFD GTAVITRAVA ADNGLTAGTD NLMPFNIVIP TSEITQPITS IKLEIVTSKS GGQ AGDQMS WSASGSLAVT IHGGNYPGAL RPVTLVAYER VATGSVVTVA GVSNFELIPN PELAKNLVTE YGRFDPGAMN YTKL ILSER DRLGIKTVWP TREYTDFREY FMEVADLNSP LKIAGA

UniProtKB: Structural polyprotein

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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: 7.2
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: 47.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3524
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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