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- EMDB-36760: Cryo-EM structure of conformation 1 of complex of Nipah virus att... -

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Basic information

Entry
Database: EMDB / ID: EMD-36760
TitleCryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
Map dataCryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
Sample
  • Complex: Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
    • Protein or peptide: Heavy chain of 1E5 Fab fragments
    • Protein or peptide: Light chain of 1E5 Fab fragments
    • Protein or peptide: Glycoprotein G
    • Protein or peptide: Glycoprotein G
KeywordsHenipavirus / Attachment glycoprotein tetramer complex / neutralizing antibody / dynamic structures / VIRAL PROTEIN
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 speciesNipah virus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSun MM
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0490000 China
CitationJournal: Nat Commun / Year: 2024
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
DepositionJul 8, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36760.png

Downloads & links

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Map

FileDownload / File: emd_36760.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036
Minimum - Maximum-0.21337882 - 0.5089947
Average (Standard dev.)0.00014640551 (±0.009898412)
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: Cryo-EM structure of conformation 1 of complex of...

Fileemd_36760_half_map_1.map
AnnotationCryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of conformation 1 of complex of...

Fileemd_36760_half_map_2.map
AnnotationCryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
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 conformation 1 of complex of Nipah virus att...

EntireName: Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
Components
  • Complex: Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
    • Protein or peptide: Heavy chain of 1E5 Fab fragments
    • Protein or peptide: Light chain of 1E5 Fab fragments
    • Protein or peptide: Glycoprotein G
    • Protein or peptide: Glycoprotein G

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Supramolecule #1: Cryo-EM structure of conformation 1 of complex of Nipah virus att...

SupramoleculeName: Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nipah virus

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Macromolecule #1: Heavy chain of 1E5 Fab fragments

MacromoleculeName: Heavy chain of 1E5 Fab fragments / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.120047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Light chain of 1E5 Fab fragments

MacromoleculeName: Light chain of 1E5 Fab fragments / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.07857 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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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: Nipah virus
Molecular weightTheoretical: 56.350121 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LADKIGTEIG PKVSLIDTSS TITIPANIGL LGSKISQSTA SINENVNEKC KFTLPPLKIH ECNISCPNPL PFREYRPQTE GVSNLVGLP NNICLQKTSN QILKPKLISY TLPVVGQSGT CITDPLLAMD EGYFAYSHLE RIGSCSRGVS KQRIIGVGEV L DRGDEVPS ...String:
LADKIGTEIG PKVSLIDTSS TITIPANIGL LGSKISQSTA SINENVNEKC KFTLPPLKIH ECNISCPNPL PFREYRPQTE GVSNLVGLP NNICLQKTSN QILKPKLISY TLPVVGQSGT CITDPLLAMD EGYFAYSHLE RIGSCSRGVS KQRIIGVGEV L DRGDEVPS LFMTNVWTPP NPNTVYHCSA VYNNEFYYVL CAVSTVGDPI LNSTYWSGSL MMTRLAVKPK SNGGGYNQHQ LA LRSIEKG RYDKVMPYGP SGIKQGDTLY FPAVGFLVRT EFKYNDSNCP ITKCQYSKPE NCRLSMGIRP NSHYILRSGL LKY NLSDGE NPKVVFIEIS DQRLSIGSPS KIYDSLGQPV FYQASFSWDT MIKFGDVLTV NPLVVNWRNN TVISRPGQSQ CPRF NTCPE ICWEGVYNDA FLIDRINWIS AGVFLDSNQT AENPVFTVFK DNEILYRAQL ASEDTNAQKT ITNCFLLKNK IWCIS LVEI YDTGDNVIRP KLFAVKIPEQ C

UniProtKB: Glycoprotein G

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Macromolecule #4: Glycoprotein G

MacromoleculeName: Glycoprotein G / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nipah virus
Molecular weightTheoretical: 6.001876 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GLADKIGTEI GPKVSLIDTS STITIPANIG LLGSKISQST ASINENVNEK CKFTLPPL

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: 1.6 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ty0

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21868

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