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- EMDB-36761: Cryo-EM structure of conformation 2 of complex of Nipah virus att... -
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Basic information
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Title | Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody | |||||||||
![]() | Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 | |||||||||
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![]() | Henipavirus / Attachment glycoprotein tetramer complex / neutralizing antibody / dynamic structures / VIRAL PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||
![]() | Sun M | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 256.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.5 KB 18.5 KB | Display Display | ![]() |
Images | ![]() | 54.5 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 475.7 MB 475.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 933.9 KB | Display | ![]() |
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Full document | ![]() | 933.5 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k0dMC ![]() 8k0cC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 | ||||||||||||||||||||
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 2 of complex of...
File | emd_36761_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of conformation 2 of complex of...
File | emd_36761_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of conformation 2 of complex of Nipah virus att...
Entire | Name: Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody |
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Components |
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-Supramolecule #1: Cryo-EM structure of conformation 2 of complex of Nipah virus att...
Supramolecule | Name: Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: The heavy chain of 1E5
Macromolecule | Name: The heavy chain of 1E5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.120047 KDa |
Recombinant expression | Organism: ![]() |
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: The light chain of 1E5
Macromolecule | Name: The light chain of 1E5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.07857 KDa |
Recombinant expression | Organism: ![]() |
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: ![]() |
Molecular weight | Theoretical: 45.227383 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: PKLISYTLPV VGQSGTCITD PLLAMDEGYF AYSHLERIGS CSRGVSKQRI IGVGEVLDRG DEVPSLFMTN VWTPPNPNTV YHCSAVYNN EFYYVLCAVS TVGDPILNST YWSGSLMMTR LAVKPKSNGG GYNQHQLALR SIEKGRYDKV MPYGPSGIKQ G DTLYFPAV ...String: PKLISYTLPV VGQSGTCITD PLLAMDEGYF AYSHLERIGS CSRGVSKQRI IGVGEVLDRG DEVPSLFMTN VWTPPNPNTV YHCSAVYNN EFYYVLCAVS TVGDPILNST YWSGSLMMTR LAVKPKSNGG GYNQHQLALR SIEKGRYDKV MPYGPSGIKQ G DTLYFPAV GFLVRTEFKY NDSNCPITKC QYSKPENCRL SMGIRPNSHY ILRSGLLKYN LSDGENPKVV FIEISDQRLS IG SPSKIYD SLGQPVFYQA SFSWDTMIKF GDVLTVNPLV VNWRNNTVIS RPGQSQCPRF NTCPEICWEG VYNDAFLIDR INW ISAGVF LDSNQTAENP VFTVFKDNEI LYRAQLASED TNAQKTITNC FLLKNKIWCI SLVEIYDTGD NVIRPKLFAV KIPE QC UniProtKB: Glycoprotein G |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134340 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |