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- PDB-8k3c: Nipah virus Attachment glycoprotein with 41-6 antibody fragment -

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Basic information

Entry
Database: PDB / ID: 8k3c
TitleNipah virus Attachment glycoprotein with 41-6 antibody fragment
Components
  • Glycoprotein G
  • Heavy chain of 41-6 Fab fragments
  • Light chain of 41-6 Fab fragment
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Nipah virus / Attachment glycoprotein / tetramer complex / Neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Henipavirus nipahense
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsSun, M.M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0490000 China
CitationJournal: Nat Commun / Year: 2024
Title: Potent human neutralizing antibodies against Nipah virus derived from two ancestral antibody heavy chains.
Authors: Li Chen / Mengmeng Sun / Huajun Zhang / Xinghai Zhang / Yanfeng Yao / Ming Li / Kangyin Li / Pengfei Fan / Haiwei Zhang / Ye Qin / Zhe Zhang / Entao Li / Zhen Chen / Wuxiang Guan / Shanshan ...Authors: Li Chen / Mengmeng Sun / Huajun Zhang / Xinghai Zhang / Yanfeng Yao / Ming Li / Kangyin Li / Pengfei Fan / Haiwei Zhang / Ye Qin / Zhe Zhang / Entao Li / Zhen Chen / Wuxiang Guan / Shanshan Li / Changming Yu / Kaiming Zhang / Rui Gong / Sandra Chiu /
Abstract: Nipah virus (NiV) is a World Health Organization priority pathogen and there are currently no approved drugs for clinical immunotherapy. Through the use of a naïve human phage-displayed Fab library, ...Nipah virus (NiV) is a World Health Organization priority pathogen and there are currently no approved drugs for clinical immunotherapy. Through the use of a naïve human phage-displayed Fab library, two neutralizing antibodies (NiV41 and NiV42) targeting the NiV receptor binding protein (RBP) were identified. Following affinity maturation, antibodies derived from NiV41 display cross-reactivity against both NiV and Hendra virus (HeV), whereas the antibody based on NiV42 is only specific to NiV. Results of immunogenetic analysis reveal a correlation between the maturation of antibodies and their antiviral activity. In vivo testing of NiV41 and its mature form (41-6) show protective efficacy against a lethal NiV challenge in hamsters. Furthermore, a 2.88 Å Cryo-EM structure of the tetrameric RBP and antibody complex demonstrates that 41-6 blocks the receptor binding interface. These findings can be beneficial for the development of antiviral drugs and the design of vaccines with broad spectrum against henipaviruses.
History
DepositionJul 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Light chain of 41-6 Fab fragment
C: Heavy chain of 41-6 Fab fragments
A: Glycoprotein G
B: Glycoprotein G


Theoretical massNumber of molelcules
Total (without water)154,0394
Polymers154,0394
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Light chain of 41-6 Fab fragment


Mass: 22844.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#2: Antibody Heavy chain of 41-6 Fab fragments


Mass: 25312.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#3: Protein Glycoprotein G


Mass: 52941.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Cell line (production host): Expi293F cells / Production host: Homo sapiens (human) / References: UniProt: Q9IH62

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of complex of attachment glycoprotein G with 41-6 Fab fragment
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Henipavirus nipahense3052225
21Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenConc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 3 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9103
Image scansWidth: 4092 / Height: 5760

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Processing

CTF correctionType: NONE
Particle selectionNum. of particles selected: 879898
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 299497 / Symmetry type: POINT

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