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Yorodumi- EMDB-41506: Human parainfluenza virus type 3 prefusion F trimer in complex wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41506 | |||||||||
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Title | Human parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Immune system / viral neutralization / VIRAL PROTEIN | |||||||||
Function / homology | Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0 Function and homology information | |||||||||
Biological species | Human respirovirus 3 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Otrelo-Cardoso AR / Jardetzky TS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To be published Title: Functional and structural characteristics of human monoclonal antibodies that potently neutralize human parainfluenza virus type 3 Authors: Suryadevara N / Otrelo-Cardoso AR / Kose N / Hu YX / Binshtein E / Wolters R / Drew-Bear J / Handal LS / Carnahan RH / Moscona A / Jardetzky TS / Crowe Jr JE | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41506.map.gz | 62.3 MB | EMDB map data format | |
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Header (meta data) | emd-41506-v30.xml emd-41506.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41506_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_41506.png | 430.5 KB | ||
Filedesc metadata | emd-41506.cif.gz | 6.1 KB | ||
Others | emd_41506_half_map_1.map.gz emd_41506_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41506 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41506 | HTTPS FTP |
-Validation report
Summary document | emd_41506_validation.pdf.gz | 906.4 KB | Display | EMDB validaton report |
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Full document | emd_41506_full_validation.pdf.gz | 906 KB | Display | |
Data in XML | emd_41506_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_41506_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41506 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41506 | HTTPS FTP |
-Related structure data
Related structure data | 8tqkMC 8tqiC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41506.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41506_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41506_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HPIV3 prefusion F trimer in complex with rPIV3-18 Fab
Entire | Name: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab |
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Components |
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-Supramolecule #1: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab
Supramolecule | Name: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human respirovirus 3 |
-Supramolecule #2: Fusion glycoprotein F0
Supramolecule | Name: Fusion glycoprotein F0 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Human respirovirus 3 |
-Supramolecule #3: rPIV3-18 light chain
Supramolecule | Name: rPIV3-18 light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #4: rPIV3-18 heavy chain
Supramolecule | Name: rPIV3-18 heavy chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Heavy chain Fab rPIV3-18
Macromolecule | Name: Heavy chain Fab rPIV3-18 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.959973 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EVQLLESGGG LVRPGGSLRL SCAASGFTFS KYVMAWVRQA PGKGLEWVSS ITSGERTFYA DSVKGRFTVS RDNSKYTLDL EMSRLRAED TAVYYCAKMF KWDYDTSDFG VWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: EVQLLESGGG LVRPGGSLRL SCAASGFTFS KYVMAWVRQA PGKGLEWVSS ITSGERTFYA DSVKGRFTVS RDNSKYTLDL EMSRLRAED TAVYYCAKMF KWDYDTSDFG VWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSC |
-Macromolecule #2: Light chain Fab rPIV3-28
Macromolecule | Name: Light chain Fab rPIV3-28 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.671273 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DFQMTQSPST LSASVGDRVT ITCRASQSVG NWLTWYQHKP GKAPKILIYK ASTLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QFNTYSWTFG QGTRVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DFQMTQSPST LSASVGDRVT ITCRASQSVG NWLTWYQHKP GKAPKILIYK ASTLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QFNTYSWTFG QGTRVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLRSPVTKS FNRGEC |
-Macromolecule #3: Fusion glycoprotein F0
Macromolecule | Name: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human respirovirus 3 |
Molecular weight | Theoretical: 57.360102 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QIDITKLQHV GVLVNSPKGM KISQNFETRY LILSLIPKIE DSNSCGDQQI KQYKRLLDRL IIPLYDGLKL QKDVIVTNQE SNENTDPRT ERFFGGVIGT IALGVATSAQ ITAAVALVEA KQAKSDIEKL KEAIRDTNKA VQSVCSSVGN CIVAIKSVQD Y VNKEIVPS ...String: QIDITKLQHV GVLVNSPKGM KISQNFETRY LILSLIPKIE DSNSCGDQQI KQYKRLLDRL IIPLYDGLKL QKDVIVTNQE SNENTDPRT ERFFGGVIGT IALGVATSAQ ITAAVALVEA KQAKSDIEKL KEAIRDTNKA VQSVCSSVGN CIVAIKSVQD Y VNKEIVPS IARLGCEAAG LQLGIALTQH YSELTNCFGD NIGSLQEKGI KLQCIASLYR TNITEIFTTS TVDKYDIYDL LF TESIKVR VIDVDLNDYS ITLQVRLPLL TRLLNTQIYK VDSISYNIQN REWYIPLPSH IMTKGAFLGG ADVKECIEAF SSY ICPSDP GFVLNHEMES CLSGNISQCP RTTVTSDIVP RYAFVNGGVV ANCITTTCTC NGIGNRINQP PDQGVKIITH KECN TIGIN GMLFNTNKEG TLAFYTPDDI TLNNSVALDP IDISIELNKV KSDLEESKEW YRRSNQKLSA IEDKIEEILS KIYHI ENEI ARIKKLIGEA PGSENLYFQG GSGSHHHHHH HH UniProtKB: Fusion glycoprotein F0 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.15 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |