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- EMDB-54918: Prefusion-stabilized Nipah virus fusion protein in complex with i... -

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Basic information

Entry
Database: EMDB / ID: EMD-54918
TitlePrefusion-stabilized Nipah virus fusion protein in complex with inhibitory nanobody F112
Map data
Sample
  • Complex: Prefusion-stabilized Nipah virus F glycoprotein in complex with the neutralizing F112 nanobody
    • Complex: Fusion glycoprotein F
      • Complex: F112 nanobody
        • Protein or peptide: F112 nanobody
      • Protein or peptide: Fusion glycoprotein F0
KeywordsFusion protein / antiviral / nanobody / VIRAL PROTEIN
Function / homologymembrane fusion involved in viral entry into host cell / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHenipavirus nipahense / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsKralova A / Hanke L
Funding supportEuropean Union, Sweden, 3 items
OrganizationGrant numberCountry
European Commission101191794European Union
European Research Council (ERC)101165699European Union
Swedish Research Council2021-01723 Sweden
CitationJournal: To Be Published
Title: Prefusion-stabilized Nipah virus fusion protein in complex with inhibitory nanobody F112
Authors: Kralova A / Hanke L
History
DepositionAug 28, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54918.png

Downloads & links

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Map

FileDownload / File: emd_54918.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.26679954 - 0.70040274
Average (Standard dev.)0.0006905394 (±0.018175047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54918_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54918_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 : Prefusion-stabilized Nipah virus F glycoprotein in complex with t...

EntireName: Prefusion-stabilized Nipah virus F glycoprotein in complex with the neutralizing F112 nanobody
Components
  • Complex: Prefusion-stabilized Nipah virus F glycoprotein in complex with the neutralizing F112 nanobody
    • Complex: Fusion glycoprotein F
      • Complex: F112 nanobody
        • Protein or peptide: F112 nanobody
      • Protein or peptide: Fusion glycoprotein F0

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Supramolecule #1: Prefusion-stabilized Nipah virus F glycoprotein in complex with t...

SupramoleculeName: Prefusion-stabilized Nipah virus F glycoprotein in complex with the neutralizing F112 nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 44 KDa

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Supramolecule #2: Fusion glycoprotein F

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

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Supramolecule #3: F112 nanobody

SupramoleculeName: F112 nanobody / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Vicugna pacos (alpaca)

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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: 62.510625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDCVGDVR LAGVCMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT ...String:
MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDCVGDVR LAGVCMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT VYVFTALQDY INTNLVPTID KIPCKQTELS LDLALSKYLS DLLFVFGPNL QDPVSNSMTI QAISQAFGGN YE TLLRTLG YATEDFDDLL ESDSITGQII YVDLSSYYII VRVYFPILTE IQQAYIQELL PVSFNNDDSE WISIVPNFIL VRN TLISNI EIGFCLITKR SVICNQDYAT PMTNNMRECL TGSTEKCPRE LVVSSHVPRF ALSNGVLFAN CISVTCQCQT TGRA ISQSG EQTLLMIDNT TCPTAVLGNV IISLGKYLGS VNYNSEGIAI GPPVFTDKVD ISSQISSMNQ SLQQSKDYIK EAQRL LDTV NPSMKQIEDK IEEILSKIYH IENEIARIKK LIGEAPGGIE GRKLHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAW SHP QFEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: F112 nanobody

MacromoleculeName: F112 nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.323876 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAVLGSIYG INAMAWYRRA PGSQRELVAV GSGDRINYAD AVKGRFTISR DDAKNSVYLQ MNSLKPEDT AVYYCQANIN TSGGWFREYW GQGTQVTVSS GGLPGTGGHH HHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration0.24 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMC4H11NO3Tris
500.0 mMC12H22O11Sucrose
0.65 mMC10H16N2O8EDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.28 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: cryoSPARC ab-initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 139202
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold
Output model

PDB-9shw:
Prefusion-stabilized Nipah virus fusion protein in complex with inhibitory nanobody F112

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