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- EMDB-36849: Nipah virus Attachment glycoprotein with 41-6 antibody fragment -

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Basic information

Entry
Database: EMDB / ID: EMD-36849
TitleNipah virus Attachment glycoprotein with 41-6 antibody fragment
Map data
Sample
  • Complex: Cryo-EM structure of complex of attachment glycoprotein G with 41-6 Fab fragment
    • Protein or peptide: Light chain of 41-6 Fab fragment
    • Protein or peptide: Heavy chain of 41-6 Fab fragments
    • Protein or peptide: Glycoprotein G
KeywordsNipah 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 speciesHenipavirus nipahense / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsSun MM
Funding support China, 1 items
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, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36849.png

Downloads & links

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Map

FileDownload / File: emd_36849.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.7599602 - 2.282065
Average (Standard dev.)0.0000062933864 (±0.031134028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36849_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36849_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of complex of attachment glycoprotein G with 41...

EntireName: Cryo-EM structure of complex of attachment glycoprotein G with 41-6 Fab fragment
Components
  • Complex: Cryo-EM structure of complex of attachment glycoprotein G with 41-6 Fab fragment
    • Protein or peptide: Light chain of 41-6 Fab fragment
    • Protein or peptide: Heavy chain of 41-6 Fab fragments
    • Protein or peptide: Glycoprotein G

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Supramolecule #1: Cryo-EM structure of complex of attachment glycoprotein G with 41...

SupramoleculeName: Cryo-EM structure of complex of attachment glycoprotein G with 41-6 Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus nipahense

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

MacromoleculeName: Light chain of 41-6 Fab fragment / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.844219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QSVVTQPPSV SAAPGQKVTI SCSGSSSNIG TNHLSWYQQV PGTAPKLLIY DNNKRPSGIP DRFSGSKSGT SASLAISGLQ SEDEADYYC ATWDDSLHAW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVVTQPPSV SAAPGQKVTI SCSGSSSNIG TNHLSWYQQV PGTAPKLLIY DNNKRPSGIP DRFSGSKSGT SASLAISGLQ SEDEADYYC ATWDDSLHAW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #2: Heavy chain of 41-6 Fab fragments

MacromoleculeName: Heavy chain of 41-6 Fab fragments / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.312264 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVQLVQSGGG LVQPGGSLRL SCAASGFTVS SNYMSWVRQA PGKGLEWVSA ISGSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD REDIVVVPAP RGYYYYYYMD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String:
EVQLVQSGGG LVQPGGSLRL SCAASGFTVS SNYMSWVRQA PGKGLEWVSA ISGSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD REDIVVVPAP RGYYYYYYMD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDKTS

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Macromolecule #3: Glycoprotein G

MacromoleculeName: Glycoprotein G / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 52.941188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ISQSTASINE NVNEKCKFTL PPLKIHECNI SCPNPLPFRE YRPQTEGVSN LVGLPNNICL QKTSNQILKP KLISYTLPVV GQSGTCITD PLLAMDEGYF AYSHLERIGS CSRGVSKQRI IGVGEVLDRG DEVPSLFMTN VWTPPNPNTV YHCSAVYNNE F YYVLCAVS ...String:
ISQSTASINE NVNEKCKFTL PPLKIHECNI SCPNPLPFRE YRPQTEGVSN LVGLPNNICL QKTSNQILKP KLISYTLPVV GQSGTCITD PLLAMDEGYF AYSHLERIGS CSRGVSKQRI IGVGEVLDRG DEVPSLFMTN VWTPPNPNTV YHCSAVYNNE F YYVLCAVS TVGDPILNST YWSGSLMMTR LAVKPKSNGG GYNQHQLALR SIEKGRYDKV MPYGPSGIKQ GDTLYFPAVG FL VRTEFKY NDSNCPITKC QYSKPENCRL SMGIRPNSHY ILRSGLLKYN LSDGENPKVV FIEISDQRLS IGSPSKIYDS LGQ PVFYQA SFSWDTMIKF GDVLTVNPLV VNWRNNTVIS RPGQSQCPRF NTCPEICWEG VYNDAFLIDR INWISAGVFL DSNQ TAENP VFTVFKDNEI LYRAQLASED TNAQKTITNC FLLKNKIWCI SLVEIYDTGD NVIRPKLFAV KIPEQC

UniProtKB: Glycoprotein G

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.16 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number real images: 9103 / Average exposure time: 3.0 sec. / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 879898
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7txz

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299497

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