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- PDB-8k0d: Cryo-EM structure of conformation 2 of complex of Nipah virus att... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k0d | ||||||
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Title | Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody | ||||||
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![]() | VIRAL PROTEIN / Henipavirus / Attachment glycoprotein tetramer complex / neutralizing antibody / dynamic structures | ||||||
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 | ELECTRON MICROSCOPY / 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 299.4 KB | Display | ![]() |
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PDB format | ![]() | 240.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 36761MC ![]() 8k0cC ![]() 8xc4C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Antibody | Mass: 26120.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 23078.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 45227.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 3 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
Image scans | Width: 4092 / Height: 5760 |
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Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134340 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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