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- EMDB-36761: Cryo-EM structure of conformation 2 of complex of Nipah virus att... -

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Basic information

Entry
Database: EMDB / ID: EMD-36761
TitleCryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody
Map dataCryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5
Sample
  • Complex: Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody
    • Protein or peptide: The heavy chain of 1E5
    • Protein or peptide: The light chain of 1E5
    • 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: 2.94 Å
AuthorsSun M
Funding support China, 1 items
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 / 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 ...Authors: Fan P / Sun M / Zhang X / Yao Y / Liu Y / Zhang H / Li M / Fang T / Sun B / 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, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36761.png

Downloads & links

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Map

FileDownload / File: emd_36761.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.2798305 - 0.6338586
Average (Standard dev.)0.000120985576 (±0.009357991)
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 2 of complex of...

Fileemd_36761_half_map_1.map
AnnotationCryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of conformation 2 of complex of...

Fileemd_36761_half_map_2.map
AnnotationCryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5
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 2 of complex of Nipah virus att...

EntireName: Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody
Components
  • Complex: Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody
    • Protein or peptide: The heavy chain of 1E5
    • Protein or peptide: The light chain of 1E5
    • Protein or peptide: Glycoprotein G

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Supramolecule #1: Cryo-EM structure of conformation 2 of complex of Nipah virus att...

SupramoleculeName: Cryo-EM structure of conformation 2 of complex of Nipah virus attachment 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: The heavy chain of 1E5

MacromoleculeName: The heavy chain of 1E5 / 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: The light chain of 1E5

MacromoleculeName: The light chain of 1E5 / 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: 45.227383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PKLISYTLPV VGQSGTCITD PLLAMDEGYF AYSHLERIGS CSRGVSKQRI IGVGEVLDRG DEVPSLFMTN VWTPPNPNTV YHCSAVYNN EFYYVLCAVS TVGDPILNST YWSGSLMMTR LAVKPKSNGG GYNQHQLALR SIEKGRYDKV MPYGPSGIKQ G DTLYFPAV ...String:
PKLISYTLPV VGQSGTCITD PLLAMDEGYF AYSHLERIGS CSRGVSKQRI IGVGEVLDRG DEVPSLFMTN VWTPPNPNTV YHCSAVYNN EFYYVLCAVS TVGDPILNST YWSGSLMMTR LAVKPKSNGG GYNQHQLALR SIEKGRYDKV MPYGPSGIKQ G DTLYFPAV GFLVRTEFKY NDSNCPITKC QYSKPENCRL SMGIRPNSHY ILRSGLLKYN LSDGENPKVV FIEISDQRLS IG SPSKIYD SLGQPVFYQA SFSWDTMIKF GDVLTVNPLV VNWRNNTVIS RPGQSQCPRF NTCPEICWEG VYNDAFLIDR INW ISAGVF LDSNQTAENP VFTVFKDNEI LYRAQLASED TNAQKTITNC FLLKNKIWCI SLVEIYDTGD NVIRPKLFAV KIPE QC

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:

8k0c

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134340

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