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Yorodumi- EMDB-41505: Hemagglutinin-neuraminidase from Human parainfluenza virus type 3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41505 | |||||||||
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Title | Hemagglutinin-neuraminidase from Human parainfluenza virus type 3: complex with rPIV3-23 and rPIV3-28 Fabs | |||||||||
Map data | DeepEMhancer output map | |||||||||
Sample |
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Keywords | Immune system / viral neutralization / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Human respirovirus 3 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 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_41505.map.gz | 51.4 MB | EMDB map data format | |
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Header (meta data) | emd-41505-v30.xml emd-41505.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41505_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_41505.png | 594.6 KB | ||
Filedesc metadata | emd-41505.cif.gz | 6.4 KB | ||
Others | emd_41505_half_map_1.map.gz emd_41505_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41505 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41505 | HTTPS FTP |
-Validation report
Summary document | emd_41505_validation.pdf.gz | 903.7 KB | Display | EMDB validaton report |
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Full document | emd_41505_full_validation.pdf.gz | 903.3 KB | Display | |
Data in XML | emd_41505_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_41505_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41505 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41505 | HTTPS FTP |
-Related structure data
Related structure data | 8tqiMC 8tqkC 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_41505.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | DeepEMhancer output map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41505_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41505_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs
Entire | Name: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs |
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Components |
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-Supramolecule #1: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs
Supramolecule | Name: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human respirovirus 3 |
-Supramolecule #2: Hemagglutinin-neuraminidase glycoprotein
Supramolecule | Name: Hemagglutinin-neuraminidase glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human respirovirus 3 |
-Supramolecule #3: Recombinant rPIV3-28 Fab
Supramolecule | Name: Recombinant rPIV3-28 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #4: Recombinant rPIV3-23 Fab
Supramolecule | Name: Recombinant rPIV3-23 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Hemagglutinin-neuraminidase
Macromolecule | Name: Hemagglutinin-neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human respirovirus 3 |
Molecular weight | Theoretical: 50.774414 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVPPQRITHD VGIKPLNPDD FWRCTSGLPS LMKTPKIRLM PGPGLLAMPT TVDGCVRTPS LVINDLIYAY TSNLITRGCQ DIGKSYQVL QIGIITVNSD LVPDLNPRIS HTFNINDNRK SCSLALLNTD VYQLCSTPKV DERSDYASSG IEDIVLDIVN H DGSISTTR ...String: EVPPQRITHD VGIKPLNPDD FWRCTSGLPS LMKTPKIRLM PGPGLLAMPT TVDGCVRTPS LVINDLIYAY TSNLITRGCQ DIGKSYQVL QIGIITVNSD LVPDLNPRIS HTFNINDNRK SCSLALLNTD VYQLCSTPKV DERSDYASSG IEDIVLDIVN H DGSISTTR FKNNNISFDQ PYAALYPSVG PGIYYKGKII FLGYGGLEHP INENAICNTT GCPGKTQRDC NQASHSPWFS DR RMVNSII VVDKGLNSIP KLKVWTISMR QNYWGSEGRL LLLGNKIYIY TRSTSWHSKL QLGIIDITDY SDIRIKWTWH NVL SRPGNN ECPWGHSCPD GCITGVYTDA YPLNPTGSIV SSVILDSQKS RVNPVITYST STERVNELAI RNKTLSAGYT TTSC ITHYN KGYCFHIVEI NHKSLDTFQP MLFKTEIPKS CSGSENLYFQ GGSHHHHHH UniProtKB: Hemagglutinin-neuraminidase |
-Macromolecule #2: Heavy chain Fab rPIV3-28
Macromolecule | Name: Heavy chain Fab rPIV3-28 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.344152 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EVKLLESGGG LIQPGDSLRL SCAASGFTFS TFAMSWVRQA PGKGLEWVSV ITSTGSSADY ADSVKGRFTM SRDNSKNTVY LQMDSLRAD DTAVYFCAKQ GATILSSFES WGQGSLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String: EVKLLESGGG LIQPGDSLRL SCAASGFTFS TFAMSWVRQA PGKGLEWVSV ITSTGSSADY ADSVKGRFTM SRDNSKNTVY LQMDSLRAD DTAVYFCAKQ GATILSSFES WGQGSLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC |
-Macromolecule #3: Light chain Fab rPIV3-28
Macromolecule | Name: Light chain Fab rPIV3-28 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.592119 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIQMTQSPSS LSASIGDRVT ITCQASQDID KYLNWYQQKP GKAPKLLIYD ASNFETGVPS RFSGSGSGTY FTFTISSLQA EDIATYYCQ QYDDLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASIGDRVT ITCQASQDID KYLNWYQQKP GKAPKLLIYD ASNFETGVPS RFSGSGSGTY FTFTISSLQA EDIATYYCQ QYDDLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLRSPVTKS FNRGEC |
-Macromolecule #4: Heavy chain Fab rPIV3-23
Macromolecule | Name: Heavy chain Fab rPIV3-23 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.95298 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QVQLQESGPG LVRPSQTLSL TCSVSGASIT DDLNRWSWIR QHPGKGLECV GYISYSGTTY YNPSLQGRLS ISLDTSRNQV SLKLTSVTA ADTAVYFCAR APIIMSSPSW GLYDQDYVPM DVWGQGTTVF VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String: QVQLQESGPG LVRPSQTLSL TCSVSGASIT DDLNRWSWIR QHPGKGLECV GYISYSGTTY YNPSLQGRLS ISLDTSRNQV SLKLTSVTA ADTAVYFCAR APIIMSSPSW GLYDQDYVPM DVWGQGTTVF VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC |
-Macromolecule #5: Light chain Fab rPIV3-23
Macromolecule | Name: Light chain Fab rPIV3-23 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.309943 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIVMTQSPAT LSVSPGERVT LSCRASQSVG SDLAWYQQKP GQAPRLLIYG ASTRATGVPA KFSGSGSGTE FTLTISGLQS EDFALYYCH QYNNWWTFGL GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String: DIVMTQSPAT LSVSPGERVT LSCRASQSVG SDLAWYQQKP GQAPRLLIYG ASTRATGVPA KFSGSGSGTE FTLTISGLQS EDFALYYCH QYNNWWTFGL GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLRSPVTKSF NRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k 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 / Cs: 2.7 mm / 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 |