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- PDB-8k0c: Cryo-EM structure of conformation 1 of complex of Nipah virus att... -

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Basic information

Entry
Database: PDB / ID: 8k0c
TitleCryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
Components
  • (Glycoprotein G) x 2
  • Heavy chain of 1E5 Fab fragments
  • Light chain of 1E5 Fab fragments
KeywordsVIRAL PROTEIN / Henipavirus / Attachment glycoprotein tetramer complex / neutralizing antibody / dynamic structures
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 speciesMacaca mulatta (Rhesus monkey)
Nipah virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSun, M.M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0490000 China
CitationJournal: 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, B.J. / Chen, Z. / Chi, X. / Chen, L. / Chen, Z. / Zhang, G. / Ren, Y. / Liu, Z. / Li, Y. / Li, J. / ...Authors: Fan, P. / Sun, M. / Zhang, X. / Yao, Y. / Liu, Y. / Zhang, H. / Li, M. / Fang, T. / Sun, B.J. / 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
DepositionJul 8, 2023Deposition site: PDBJ / Processing site: PDBC
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
E: Heavy chain of 1E5 Fab fragments
F: Light chain of 1E5 Fab fragments
A: Glycoprotein G
C: Glycoprotein G
G: Heavy chain of 1E5 Fab fragments
H: Light chain of 1E5 Fab fragments
B: Glycoprotein G
D: Glycoprotein G


Theoretical massNumber of molelcules
Total (without water)223,1018
Polymers223,1018
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Sample particle shape and size
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Heavy chain of 1E5 Fab fragments


Mass: 26120.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody Light chain of 1E5 Fab fragments


Mass: 23078.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein Glycoprotein G


Mass: 56350.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Gene: G / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9IH62
#4: Protein Glycoprotein G


Mass: 6001.876 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Gene: G / Cell line (production host): Expi293F / 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 conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightUnits: KILODALTONS/NANOMETER
Source (natural)Organism: Nipah virus
Source (recombinant)Organism: Homo sapiens (human)
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: 1600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 4092 / Height: 5760

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Processing

EM softwareName: cryoSPARC / Version: 3.2.0 / Category: particle selection
CTF correctionType: NONE
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21868 / Symmetry type: POINT

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