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Yorodumi- EMDB-38504: Nipah virus fusion glycoprotein in complex with a broadly neutral... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38504 | |||||||||
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Title | Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Henipavirus / Fusion glycoprotein / Antibody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Henipavirus nipahense / Macaca (macaques) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Fan PF / Ren Y / Yu CM / Chen W | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6 Authors: Fan PF / Yu CM / Chen W / Ren Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38504.map.gz | 212.2 MB | EMDB map data format | |
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Header (meta data) | emd-38504-v30.xml emd-38504.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38504_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_38504.png | 119.1 KB | ||
Filedesc metadata | emd-38504.cif.gz | 5.7 KB | ||
Others | emd_38504_half_map_1.map.gz emd_38504_half_map_2.map.gz | 391.9 MB 391.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38504 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38504 | HTTPS FTP |
-Validation report
Summary document | emd_38504_validation.pdf.gz | 850 KB | Display | EMDB validaton report |
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Full document | emd_38504_full_validation.pdf.gz | 849.6 KB | Display | |
Data in XML | emd_38504_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | emd_38504_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38504 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38504 | HTTPS FTP |
-Related structure data
Related structure data | 8xnhMC 8xn9C 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_38504.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38504_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38504_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nipah virus fusion glycoprotein in complex with a broadly neutral...
Entire | Name: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8 |
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Components |
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-Supramolecule #1: Nipah virus fusion glycoprotein in complex with a broadly neutral...
Supramolecule | Name: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: Nipah virus fusion glycoprotein
Supramolecule | Name: Nipah virus fusion glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Henipavirus nipahense |
-Supramolecule #3: 5C8 Fab
Supramolecule | Name: 5C8 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Macaca (macaques) |
-Macromolecule #1: Fusion glycoprotein F0
Macromolecule | Name: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Henipavirus nipahense |
Molecular weight | Theoretical: 55.073988 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ ...String: ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ TELSLDLALS KYLSDLLFVF GPNLQDPVSN SMTIQAISQA FGGNYETLLR TLGYATEDFD DLLESDSITG QI IYVDLSS YYIIVRVYFP ILTEIQQAYI QELLPVSFNN DNSEWISIVP NFILVRNTLI SNIEIGFCLI TKRSVICNQD YAT PMTNNM RECLTGSTEK CPRELVVSSH VPRFALSNGV LFANCISVTC QCQTTGRAIS QSGEQTLLMI DNTTCPTAVL GNVI ISLGK YLGSVNYNSE GIAIGPPVFT DKVDISSQIS SMNQSLQQSK DYIKEAQRLL DGTMKQIEDK IEEILSKIYH IENEI ARIK KLIGEGGSHH HHHH UniProtKB: Fusion glycoprotein F0 |
-Macromolecule #2: 5C8-VL
Macromolecule | Name: 5C8-VL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca (macaques) |
Molecular weight | Theoretical: 14.00351 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQLTQSPSS LSASVGDTVT ITCQASQGIG NNLHWYQQKP GKAPKLLIYR ASSLQSGIPS RFSGSGSGTD YTLTISSLQP EDFAYYCQQ GYSYPFTFGP GTKVDIKRTV AAPSVFIFPP SDEQLKSGTA SV |
-Macromolecule #3: 5C8-VH
Macromolecule | Name: 5C8-VH / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca (macaques) |
Molecular weight | Theoretical: 14.331 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG VVKPSETLSL TCAVSGGSIS DSYRWSWIRQ PPGKGLEWIG YIYGSSTSTN YNPSLKSRVT ISKDTSKNQF SLNLSSLTA ADTAVYYCVR VVQYLEWFVD LIEVNWFDVW GPGVLVTVSS A |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.015 mg/mL |
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Buffer | pH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.91 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: 1.8 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |