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- EMDB-38499: Nipah virus fusion glycoprotein in complex with a broadly neutral... -

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Basic information

Entry
Database: EMDB / ID: EMD-38499
TitleNipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Map data
Sample
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 1D6 Fab
      • Protein or peptide: 1D6 VH
      • Protein or peptide: 1D6 VL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHenipavirus / Fusion glycoprotein / Antibody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHenipavirus nipahense / Macaca (macaques)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsFan PF / Ren Y / Yu CM / Chen W
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentJCKY2020802B001 China
CitationJournal: To Be Published
Title: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Authors: Fan PF / Yu CM / Chen W / Ren Y
History
DepositionDec 29, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_38499.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.74 Å
Density
Contour LevelBy AUTHOR: 0.173
Minimum - Maximum-2.252557 - 4.071979
Average (Standard dev.)0.000012893443 (±0.07589831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 340.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nipah virus fusion glycoprotein in complex with a broadly neutral...

EntireName: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Components
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 1D6 Fab
      • Protein or peptide: 1D6 VH
      • Protein or peptide: 1D6 VL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Nipah virus fusion glycoprotein in complex with a broadly neutral...

SupramoleculeName: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #2: Nipah virus fusion glycoprotein

SupramoleculeName: Nipah virus fusion glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #3: 1D6 Fab

SupramoleculeName: 1D6 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Macaca (macaques)

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 55.418305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGGILHYEK LSKIGLVKGV TRKYKIKSNP LTKDIVIKMI PNVSNMSQCT GSVMENYKTR LNGILTPIKG ALEIYKNNTH DLVGDVRLA GVIMAGVAIG IATAAQITAG VALYEAMKNA DNINKLKSSI ESTNEAVVKL QETAEKTVYV LTALQDYINT N LVPTIDKI ...String:
ETGGILHYEK LSKIGLVKGV TRKYKIKSNP LTKDIVIKMI PNVSNMSQCT GSVMENYKTR LNGILTPIKG ALEIYKNNTH DLVGDVRLA GVIMAGVAIG IATAAQITAG VALYEAMKNA DNINKLKSSI ESTNEAVVKL QETAEKTVYV LTALQDYINT N LVPTIDKI SCKQTELSLD LALSKYLSDL LFVFGPNLQD PVSNSMTIQA ISQAFGGNYE TLLRTLGYAT EDFDDLLESD SI TGQIIYV DLSSYYIIVR VYFPILTEIQ QAYIQELLPV SFNNDNSEWI SIVPNFILVR NTLISNIEIG FCLITKRSVI CNQ DYATPM TNNMRECLTG STEKCPRELV VSSHVPRFAL SNGVLFANCI SVTCQCQTTG RAISQSGEQT LLMIDNTTCP TAVL GNVII SLGKYLGSVN YNSEGIAIGP PVFTDKVDIS SQISSMNQSL QQSKDYIKEA QRLLDGTMKQ IEDKIEEILS KIYHI ENEI ARIKKLIGEG GSHHHHHH

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: 1D6 VH

MacromoleculeName: 1D6 VH / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 22.08533 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PVLTQPPSAS EAARKSVTIS CSGSSSNIGS NSVSWYQQLP GTALKLLISY NDQRASGVSD RFSGSKSGTS ASLAISGLQT EDEADYYCA AWDDSLSGPV FGGGTRLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS ...String:
PVLTQPPSAS EAARKSVTIS CSGSSSNIGS NSVSWYQQLP GTALKLLISY NDQRASGVSD RFSGSKSGTS ASLAISGLQT EDEADYYCA AWDDSLSGPV FGGGTRLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS KQSNNKYAAS SYLSLTPEQW KSHKSYSCQV THEGSTVEKT VAP

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Macromolecule #3: 1D6 VL

MacromoleculeName: 1D6 VL / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 25.657705 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCTVSGASIS SYWWGWIRQP PGKGLEWIAD IYPNSGSTNY NPSLKSRVTN SKDASKNQFS LKLSSVTAA DTAMYYCARA PRGYSYSYVF GHRFDVWGPG VLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLQESGPG LVKPSETLSL TCTVSGASIS SYWWGWIRQP PGKGLEWIAD IYPNSGSTNY NPSLKSRVTN SKDASKNQFS LKLSSVTAA DTAMYYCARA PRGYSYSYVF GHRFDVWGPG VLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTHHHHHH H

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1141639
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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