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- EMDB-63983: Nipah virus fusion glycoprotein in complex with a broadly neutral... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63983
TitleNipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
Map data
Sample
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5C8 Fab
      • Protein or peptide: 5C8-VL
      • Protein or peptide: 5C8-VH
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsHenipavirus / Fusion glycoprotein / Antibody / ANTIVIRAL PROTEIN / VIRAL PROTEIN / VIRAL 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: 2.22 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
DepositionMar 31, 2025-
SupersessionApr 9, 2025ID: EMD-38504
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63983.png

Downloads & links

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Map

FileDownload / File: emd_63983.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.212
Minimum - Maximum-2.2779236 - 4.1272464
Average (Standard dev.)-0.00015599444 (±0.08184043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63983_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63983_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 : Nipah virus fusion glycoprotein in complex with a broadly neutral...

EntireName: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
Components
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5C8 Fab
      • Protein or peptide: 5C8-VL
      • Protein or peptide: 5C8-VH
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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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 5C8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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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: 5C8 Fab

SupramoleculeName: 5C8 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: 48.823887 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ ...String:
ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ TELSLDLALS KYLSDLLFVF GPNLQDPVSN SMTIQAISQA FGGNYETLLR TLGYATEDFD DLLESDSITG QI IYVDLSS YYIIVRVYFP ILTEIQQAYI QELLPVSFNN DNSEWISIVP NFILVRNTLI SNIEIGFCLI TKRSVICNQD YAT PMTNNM RECLTGSTEK CPRELVVSSH VPRFALSNGV LFANCISVTC QCQTTGRAIS QSGEQTLLMI DNTTCPTAVL GNVI ISLGK YLGSVNYNSE GIAIGPPVFT DKVDISSQIS SMNQSLQQSK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: 5C8-VL

MacromoleculeName: 5C8-VL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 11.414602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPSS LSASVGDTVT ITCQASQGIG NNLHWYQQKP GKAPKLLIYR ASSLQSGIPS RFSGSGSGTD YTLTISSLQP EDFAYYCQQ GYSYPFTFGP GTKVDIK

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Macromolecule #3: 5C8-VH

MacromoleculeName: 5C8-VH / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 14.085766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG VVKPSETLSL TCAVSGGSIS DSYRWSWIRQ PPGKGLEWIG YIYGSSTSTN YNPSLKSRVT ISKDTSKNQF SLNLSSLTA ADTAVYYCVR VVQYLEWFVD LIEVNWFDVW GPGVLVTV

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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: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 340 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.015 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: 51.91 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 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: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 462582
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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