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Yorodumi- EMDB-36760: Cryo-EM structure of conformation 1 of complex of Nipah virus att... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36760 | |||||||||
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Title | Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody | |||||||||
Map data | Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody | |||||||||
Sample |
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Keywords | Henipavirus / Attachment glycoprotein tetramer complex / neutralizing antibody / dynamic structures / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Nipah virus / Macaca mulatta (Rhesus monkey) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Sun MM | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Potent Henipavirus neutralizing antibody reveals dynamic structures and trigger sites of the G-tetramer Authors: Fan P / Sun M / Zhang X / Yao Y / Liu Y / Zhang H / Li M / Fang T / Sun BJ / Chen Z / Chi X / Chen L / Chen Z / Zhang G / Ren Y / Liu Z / Li Y / Li J / Li E / Guan W / Li S / Gong R / Zhang ...Authors: Fan P / Sun M / Zhang X / Yao Y / Liu Y / Zhang H / Li M / Fang T / Sun BJ / Chen Z / Chi X / Chen L / Chen Z / Zhang G / Ren Y / Liu Z / Li Y / Li J / Li E / Guan W / Li S / Gong R / Zhang K / Yu C / Chen W / Chiu S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36760.map.gz | 255 MB | EMDB map data format | |
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Header (meta data) | emd-36760-v30.xml emd-36760.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
Images | emd_36760.png | 65.2 KB | ||
Filedesc metadata | emd-36760.cif.gz | 6.1 KB | ||
Others | emd_36760_half_map_1.map.gz emd_36760_half_map_2.map.gz | 474.1 MB 474.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36760 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36760 | HTTPS FTP |
-Related structure data
Related structure data | 8k0cMC 8k0dC 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_36760.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM structure of conformation 1 of complex of...
File | emd_36760_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of conformation 1 of complex of...
File | emd_36760_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of conformation 1 of complex of Nipah virus att...
Entire | Name: Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody |
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Components |
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-Supramolecule #1: Cryo-EM structure of conformation 1 of complex of Nipah virus att...
Supramolecule | Name: Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Nipah virus |
-Macromolecule #1: Heavy chain of 1E5 Fab fragments
Macromolecule | Name: Heavy chain of 1E5 Fab fragments / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 26.120047 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG VVKPSETLSL TCAVSGGSIS DTYRWSWIRQ PPGKGLEWIG YIYGSATSTY YNPSLSSRVT ISKDMSKNQF SLNLNSVTA ADTAVYYCAR DYQYYYSGSY PTPHNWFDVW GPGVLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String: QVQLQESGPG VVKPSETLSL TCAVSGGSIS DTYRWSWIRQ PPGKGLEWIG YIYGSATSTY YNPSLSSRVT ISKDMSKNQF SLNLNSVTA ADTAVYYCAR DYQYYYSGSY PTPHNWFDVW GPGVLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSGLGTQ TYICNVNHKP SNTKVDKKVE PKSCDKTHHH HH HH |
-Macromolecule #2: Light chain of 1E5 Fab fragments
Macromolecule | Name: Light chain of 1E5 Fab fragments / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 23.07857 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQGII DYLSWYQQKP GKAPKLLIST ASNLESGVPS RFSGSGSGTE FTLTISSLQP EDFATYSCL QGYTTPYTFG QGTKVEIKTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String: DIQMTQSPSS LSASVGDRVT ITCRASQGII DYLSWYQQKP GKAPKLLIST ASNLESGVPS RFSGSGSGTE FTLTISSLQP EDFATYSCL QGYTTPYTFG QGTKVEIKTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC |
-Macromolecule #3: Glycoprotein G
Macromolecule | Name: Glycoprotein G / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Nipah virus |
Molecular weight | Theoretical: 56.350121 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LADKIGTEIG PKVSLIDTSS TITIPANIGL LGSKISQSTA SINENVNEKC KFTLPPLKIH ECNISCPNPL PFREYRPQTE GVSNLVGLP NNICLQKTSN QILKPKLISY TLPVVGQSGT CITDPLLAMD EGYFAYSHLE RIGSCSRGVS KQRIIGVGEV L DRGDEVPS ...String: LADKIGTEIG PKVSLIDTSS TITIPANIGL LGSKISQSTA SINENVNEKC KFTLPPLKIH ECNISCPNPL PFREYRPQTE GVSNLVGLP NNICLQKTSN QILKPKLISY TLPVVGQSGT CITDPLLAMD EGYFAYSHLE RIGSCSRGVS KQRIIGVGEV L DRGDEVPS LFMTNVWTPP NPNTVYHCSA VYNNEFYYVL CAVSTVGDPI LNSTYWSGSL MMTRLAVKPK SNGGGYNQHQ LA LRSIEKG RYDKVMPYGP SGIKQGDTLY FPAVGFLVRT EFKYNDSNCP ITKCQYSKPE NCRLSMGIRP NSHYILRSGL LKY NLSDGE NPKVVFIEIS DQRLSIGSPS KIYDSLGQPV FYQASFSWDT MIKFGDVLTV NPLVVNWRNN TVISRPGQSQ CPRF NTCPE ICWEGVYNDA FLIDRINWIS AGVFLDSNQT AENPVFTVFK DNEILYRAQL ASEDTNAQKT ITNCFLLKNK IWCIS LVEI YDTGDNVIRP KLFAVKIPEQ C UniProtKB: Glycoprotein G |
-Macromolecule #4: Glycoprotein G
Macromolecule | Name: Glycoprotein G / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Nipah virus |
Molecular weight | Theoretical: 6.001876 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GLADKIGTEI GPKVSLIDTS STITIPANIG LLGSKISQST ASINENVNEK CKFTLPPL UniProtKB: Glycoprotein G |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.16 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 |
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 / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Average exposure time: 3.0 sec. / Average electron dose: 51.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21868 |