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- EMDB-26163: Nipah Virus attachment (G) glycoprotein ectodomain in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-26163
TitleNipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment (local refinement of the stalk region)
Map data
Sample
  • Complex: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment
    • Protein or peptide: Glycoprotein G
    • Protein or peptide: Igh protein
    • Protein or peptide: nAH Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNiV / NiVG / attachment protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / 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 / identical protein binding / membrane / metal ion binding
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Igh protein / Glycoprotein G
Similarity search - Component
Biological speciesNipah henipavirus / Mus sp. (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang ZQ / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Science / Year: 2022
Title: Architecture and antigenicity of the Nipah virus attachment glycoprotein.
Authors: Zhaoqian Wang / Moushimi Amaya / Amin Addetia / Ha V Dang / Gabriella Reggiano / Lianying Yan / Andrew C Hickey / Frank DiMaio / Christopher C Broder / David Veesler /
Abstract: Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness. The entry of HNVs into host cells requires the attachment ...Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness. The entry of HNVs into host cells requires the attachment (G) and fusion (F) glycoproteins, which are the main targets of antibody responses. To understand viral infection and host immunity, we determined a cryo-electron microscopy structure of the NiV G homotetrameric ectodomain in complex with the nAH1.3 broadly neutralizing antibody Fab fragment. We show that a cocktail of two nonoverlapping G-specific antibodies neutralizes NiV and HeV synergistically and limits the emergence of escape mutants. Analysis of polyclonal serum antibody responses elicited by vaccination of macaques with NiV G indicates that the receptor binding head domain is immunodominant. These results pave the way for implementing multipronged therapeutic strategies against these deadly pathogens.
History
DepositionFeb 10, 2022-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ty0
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_26163.png

Downloads & links

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Map

FileDownload / File: emd_26163.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 460 pix.
= 483. Å		1.05 Å/pix.
x 460 pix.
= 483. Å		1.05 Å/pix.
x 460 pix.
= 483. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-4.9963303 - 12.855078000000001
Average (Standard dev.)-0.00044530877 (±0.06176073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 482.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z483.000483.000483.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-4.99612.855-0.000

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Supplemental data

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Additional map: #1

Fileemd_26163_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26163_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26163_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Nipah Virus attachment protein ectodomain in complex with nAH1.3 ...

EntireName: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment
Components
  • Complex: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment
    • Protein or peptide: Glycoprotein G
    • Protein or peptide: Igh protein
    • Protein or peptide: nAH Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Nipah Virus attachment protein ectodomain in complex with nAH1.3 ...

SupramoleculeName: Nipah Virus attachment protein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Nipah henipavirus

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Macromolecule #1: Glycoprotein G

MacromoleculeName: Glycoprotein G / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nipah henipavirus
Molecular weightTheoretical: 60.358535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHIQNY TRSTDNQAVI KDALQGIQQQ IKGLADKIGT EIGPKVSLID TSSTITIPAN IGLLGSKISQ STASINENVN EKCKFTLPP LKIHECNISC PNPLPFREYR PQTEGVSNLV GLPNNICLQK TSNQILKPKL ISYTLPVVGQ SGTCITDPLL A MDEGYFAY ...String:
HHHHHHIQNY TRSTDNQAVI KDALQGIQQQ IKGLADKIGT EIGPKVSLID TSSTITIPAN IGLLGSKISQ STASINENVN EKCKFTLPP LKIHECNISC PNPLPFREYR PQTEGVSNLV GLPNNICLQK TSNQILKPKL ISYTLPVVGQ SGTCITDPLL A MDEGYFAY SHLERIGSCS RGVSKQRIIG VGEVLDRGDE VPSLFMTNVW TPPNPNTVYH CSAVYNNEFY YVLCAVSTVG DP ILNSTYW SGSLMMTRLA VKPKSNGGGY NQHQLALRSI EKGRYDKVMP YGPSGIKQGD TLYFPAVGFL VRTEFKYNDS NCP ITKCQY SKPENCRLSM GIRPNSHYIL RSGLLKYNLS DGENPKVVFI EISDQRLSIG SPSKIYDSLG QPVFYQASFS WDTM IKFGD VLTVNPLVVN WRNNTVISRP GQSQCPRFNT CPEICWEGVY NDAFLIDRIN WISAGVFLDS NQTAENPVFT VFKDN EILY RAQLASEDTN AQKTITNCFL LKNKIWCISL VEIYDTGDNV IRPKLFAVKI PEQCY

UniProtKB: Glycoprotein G

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Macromolecule #2: Igh protein

MacromoleculeName: Igh protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 50.643941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVKLEESGGG LVQPGGSMKL SCVASGFSFS YYWMNWVRQS PEKGLEWVAE IRLKSNNYGT HYAESVKGRF TISRDDSKSS VYLQMNNLR PEDTGIYYCT RVITTVFAYW GQGTLVTVSA AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String:
EVKLEESGGG LVQPGGSMKL SCVASGFSFS YYWMNWVRQS PEKGLEWVAE IRLKSNNYGT HYAESVKGRF TISRDDSKSS VYLQMNNLR PEDTGIYYCT RVITTVFAYW GQGTLVTVSA AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VPSSTWPSET VTCNVAHPAS STKVDKKIVP RDCGCKPCIC TVPEVSSVFI FP PKPKDVL TITLTPKVTC VVVDISKDDP EVQFSWFVDD VEVHTAQTQP REEQFNSTFR SVSELPIMHQ DWLNGKEFKC RVN SAAFPA PIEKTISKTK GRPKAPQVYT IPPPKEQMAK DKVSLTCMIT DFFPEDITVE WQWNGQPAEN YKNTQPIMDT DGSY FVYSK LNVQKSNWEA GNTFTCSVLH EGLHNHHTEK SLSHSPGKGG SGGGSWSHPQ FEK

UniProtKB: Igh protein

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Macromolecule #3: nAH Fab light chain

MacromoleculeName: nAH Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 23.947473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVLTQSPAS LAVSLGQRAT ISCRASESVH DYGISFMNWF QQKPGQPPKL LIYSASNQGS GVPARFSGSG SGTDFSLNIH PMEEDDIAM YFCQQSKEVP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
DIVLTQSPAS LAVSLGQRAT ISCRASESVH DYGISFMNWF QQKPGQPPKL LIYSASNQGS GVPARFSGSG SGTDFSLNIH PMEEDDIAM YFCQQSKEVP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
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:

3d11

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168035
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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