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- EMDB-54916: Prefusion-stabilized Hendra virus fusion protein in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54916
TitlePrefusion-stabilized Hendra virus fusion protein in complex with inhibitory nanobody F123
Map data
Sample
  • Complex: Prefusion-stabilized Hendra virus F glycoprotein in complex with the neutralizing F123 nanobody
    • Complex: Fusion glycoprotein F
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: F123 nanobody
      • Protein or peptide: F123 nanobody
KeywordsFusion protein / antiviral / nanobody / VIRAL PROTEIN
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / host cell surface / 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 hendraense / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 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: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Tristan Ian Croll /
Abstract: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density ...This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
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_54916.png

Downloads & links

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Map

FileDownload / File: emd_54916.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 416 pix.
= 269.568 Å		0.65 Å/pix.
x 416 pix.
= 269.568 Å		0.65 Å/pix.
x 416 pix.
= 269.568 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0735
Minimum - Maximum-0.15040939 - 0.36834812
Average (Standard dev.)-0.00016026171 (±0.0104330955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 269.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54916_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_54916_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Prefusion-stabilized Hendra virus F glycoprotein in complex with ...

EntireName: Prefusion-stabilized Hendra virus F glycoprotein in complex with the neutralizing F123 nanobody
Components
  • Complex: Prefusion-stabilized Hendra virus F glycoprotein in complex with the neutralizing F123 nanobody
    • Complex: Fusion glycoprotein F
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: F123 nanobody
      • Protein or peptide: F123 nanobody

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

SupramoleculeName: Prefusion-stabilized Hendra virus F glycoprotein in complex with the neutralizing F123 nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus hendraense
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 hendraense

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Supramolecule #3: F123 nanobody

SupramoleculeName: F123 nanobody / type: complex / ID: 3 / Parent: 1 / 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 hendraense
Molecular weightTheoretical: 62.128156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATQEVRLKC LLCGIIVLVL SLEGLGILHY EKLSKIGLVK GITRKYKIKS NPLTKDIVIK MIPNVSNVSK CTGTVMENYK SRLTGILSP IKGAIELYNN NTHDCVGDVK LAGVCMAGIA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT ...String:
MATQEVRLKC LLCGIIVLVL SLEGLGILHY EKLSKIGLVK GITRKYKIKS NPLTKDIVIK MIPNVSNVSK CTGTVMENYK SRLTGILSP IKGAIELYNN NTHDCVGDVK LAGVCMAGIA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT VYVFTALQDY INTNLVPTID QIPCKQTELA LDLALSKYLS DLLFVFGPNL QDPVSNSMTI QAISQAFGGN YE TLLRTLG YATEDFDDLL ESDSIAGQIV YVDLSSYYII VRVYFPILTE IQQAYVQELL PVSFNNDNSE WISIVPNFVL IRN TLISNI EVKYCLITKK SVICNQDYAT PMTASVRECL TGSTDKCPRE LVVSSHVPRF ALSGGVLFAN CISVTCQCQT TGRA ISQSG EQTLLMIDNT TCTTVVLGNI IISLGKYLGS INYNSESIAV GPPVYTDKVD ISSQISSMNQ SLQQSKDYIK EAQKI LDTV NPSMKQIEDK IEEILSKIYH IENEIARIKK LIGEAPGGIE GRKLHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAW SHP QFEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: F123 nanobody

MacromoleculeName: F123 nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.602279 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAASGSTAD YVMGWYRQAP GKQRDLVARI TNGGSTQYAD SVKGRFTISR DNAKNTVYLQ MNSLKPEDT AVYYCNADPI WTIATMKRMG YWGEGTLVTV SSGGLPETGG HHHHHH

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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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
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: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 494292
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: Other / Chain - Initial model type: in silico model / Details: The initial model was generated using ModelAngelo
Output model

PDB-9shv:
Prefusion-stabilized Hendra virus fusion protein in complex with inhibitory nanobody F123

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