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- EMDB-54813: Prefusion-stabilized Hendra virus fusion protein in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54813
TitlePrefusion-stabilized Hendra virus fusion protein in complex with inhibitory nanobody F130
Map data
Sample
  • Complex: Prefusion-stabilized Hendra virus F glycoprotein in complex with the neutralizing F130 nanobody
    • Complex: Fusion glycoprotein F
      • Complex: F130 nanobody
        • Protein or peptide: F130 nanobody
      • Protein or peptide: Fusion glycoprotein F0
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: 2.6 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
Citation
Journal: Nat Methods / Year: 2020
Title: Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction.
Authors: Ali Punjani / Haowei Zhang / David J Fleet /
Abstract: Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are ...Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability negatively impacts computational three-dimensional (3D) reconstruction with existing iterative refinement algorithms that assume rigidity. We introduce non-uniform refinement, an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps during refinement to account for spatial variability. Unlike common shift-invariant regularizers, non-uniform refinement systematically removes noise from disordered regions, while retaining signal useful for aligning particle images, yielding dramatically improved resolution and 3D map quality in many cases. We obtain high-resolution reconstructions for multiple membrane proteins as small as 100 kDa, demonstrating increased effectiveness of cryo-EM for this class of targets critical in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package.
#2: Journal: bioRxiv / Year: 2023
Title: Automated model building and protein identification in cryo-EM maps.
Authors: Jamali K / Kall L / Zhang R / Brown A / Kimanius D / Scheres SHW
History
DepositionAug 19, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54813.png

Downloads & links

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Map

FileDownload / File: emd_54813.map.gz / Format: CCP4 / Size: 325 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 440 pix.
= 285.12 Å		0.65 Å/pix.
x 440 pix.
= 285.12 Å		0.65 Å/pix.
x 440 pix.
= 285.12 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: 0.0774
Minimum - Maximum-0.19135565 - 0.46372584
Average (Standard dev.)-0.00014131 (±0.010957975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 285.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54813_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_54813_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 Hendra virus F glycoprotein in complex with ...

EntireName: Prefusion-stabilized Hendra virus F glycoprotein in complex with the neutralizing F130 nanobody
Components
  • Complex: Prefusion-stabilized Hendra virus F glycoprotein in complex with the neutralizing F130 nanobody
    • Complex: Fusion glycoprotein F
      • Complex: F130 nanobody
        • Protein or peptide: F130 nanobody
      • Protein or peptide: Fusion glycoprotein F0

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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 F130 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: F130 nanobody

SupramoleculeName: F130 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 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: F130 nanobody

MacromoleculeName: F130 nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.742349 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLVETGGG LVQPGGSLRL SCAASEFTLS RYVVTWYRQA PGKERVFIAR IANAGGSTVY ASSVKGRFTI SRDDAKDTVY LQMDNLKPE DTAVYYCNAQ RVALTISPND GYWGQGTQVT VSSGGLPETG GHHHHHH

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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 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 482793
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-9sf4:
Prefusion-stabilized Hendra virus fusion protein in complex with inhibitory nanobody F130

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