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Yorodumi- EMDB-36760: Cryo-EM structure of conformation 1 of complex of Nipah virus att... -
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-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 / identical protein binding / membrane 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: Nat Commun / Year: 2024 Title: A potent Henipavirus cross-neutralizing antibody reveals a dynamic fusion-triggering pattern of the G-tetramer. Authors: Pengfei Fan / Mengmeng Sun / Xinghai Zhang / Huajun Zhang / Yujiao Liu / Yanfeng Yao / Ming Li / Ting Fang / Bingjie Sun / Zhengshan Chen / Xiangyang Chi / Li Chen / Cheng Peng / Zhen Chen / ...Authors: Pengfei Fan / Mengmeng Sun / Xinghai Zhang / Huajun Zhang / Yujiao Liu / Yanfeng Yao / Ming Li / Ting Fang / Bingjie Sun / Zhengshan Chen / Xiangyang Chi / Li Chen / Cheng Peng / Zhen Chen / Guanying Zhang / Yi Ren / Zixuan Liu / Yaohui Li / Jianmin Li / Entao Li / Wuxiang Guan / Shanshan Li / Rui Gong / Kaiming Zhang / Changming Yu / Sandra Chiu / Abstract: The Hendra and Nipah viruses (HNVs) are highly pathogenic pathogens without approved interventions for human use. In addition, the interaction pattern between the attachment (G) and fusion (F) ...The Hendra and Nipah viruses (HNVs) are highly pathogenic pathogens without approved interventions for human use. In addition, the interaction pattern between the attachment (G) and fusion (F) glycoproteins required for virus entry remains unclear. Here, we isolate a panel of Macaca-derived G-specific antibodies that cross-neutralize HNVs via multiple mechanisms. The most potent antibody, 1E5, confers adequate protection against the Nipah virus challenge in female hamsters. Crystallography demonstrates that 1E5 has a highly similar binding pattern to the receptor. In cryo-electron microscopy studies, the tendency of 1E5 to bind to the upper or lower heads results in two distinct quaternary structures of G. Furthermore, we identify the extended outer loop β1S2-β1S3 of G and two pockets on the apical region of fusion (F) glycoprotein as the essential sites for G-F interactions. This work highlights promising drug candidates against HNVs and contributes deeper insights into the viruses. | |||||||||
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 | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_36760.png | 65.2 KB | ||
Filedesc metadata | emd-36760.cif.gz | 6.2 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 |
-Validation report
Summary document | emd_36760_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_36760_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_36760_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_36760_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36760 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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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 |
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: 3.2 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
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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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21868 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |