+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32102 | |||||||||
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Title | Structure of infectious bursal disease virus Gx strain | |||||||||
Map data | ||||||||||
Sample |
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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 / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | IBDV, Gumboro disease virus / Infectious bursal disease virus (Gumboro virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Bao KY / Zhu P | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32102.map.gz | 275.2 MB | EMDB map data format | |
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Header (meta data) | emd-32102-v30.xml emd-32102.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_32102.png | 210.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32102 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32102 | HTTPS FTP |
-Related structure data
Related structure data | 7vrpMC 7vrnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32102.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Infectious bursal disease virus
Entire | Name: Infectious bursal disease virus (Gumboro virus) |
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Components |
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-Supramolecule #1: Infectious bursal disease virus
Supramolecule | Name: 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 |
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Host (natural) | Organism: Gallus gallus (chicken) |
-Macromolecule #1: Structural polyprotein
Macromolecule | Name: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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Source (natural) | Organism: IBDV, Gumboro disease virus |
Molecular weight | Theoretical: 47.028871 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: RANDOM ASSIGNMENT |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3524 |