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- EMDB-64753: A broad-spectrum neutralizing antibody targeting the F protein of... -

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Basic information

Entry
Database: EMDB / ID: EMD-64753
TitleA broad-spectrum neutralizing antibody targeting the F protein of NiV and HeV
Map data
Sample
  • Complex: The complex of fusion glycoprotein of Nipah virus and C-type nanoantibodies
    • Complex: Fusion glycoprotein of Nipah virus
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: C-type nanoantibodies targeting NiV and HeV fusion proteins
      • Protein or peptide: C-type nanoantibody
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsC-type nanoantibody / Nipah virus / Hendra virus / fusion glycoprotein / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Homo sapiens (human) / Nipah virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang S / Rao G / Cao S / Gong R
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
CitationJournal: To Be Published
Title: A broad-spectrum neutralizing antibody targeting the F protein of NiV and HeV
Authors: Wang S / Rao G / Cao S / Gong R
History
DepositionMay 21, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64753.png

Downloads & links

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Map

FileDownload / File: emd_64753.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.)
0.95 Å/pix.
x 440 pix.
= 418. Å		0.95 Å/pix.
x 440 pix.
= 418. Å		0.95 Å/pix.
x 440 pix.
= 418. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.7960253 - 1.260468
Average (Standard dev.)-0.00015876259 (±0.034309797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 418.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64753_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_64753_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 : The complex of fusion glycoprotein of Nipah virus and C-type nano...

EntireName: The complex of fusion glycoprotein of Nipah virus and C-type nanoantibodies
Components
  • Complex: The complex of fusion glycoprotein of Nipah virus and C-type nanoantibodies
    • Complex: Fusion glycoprotein of Nipah virus
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: C-type nanoantibodies targeting NiV and HeV fusion proteins
      • Protein or peptide: C-type nanoantibody
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The complex of fusion glycoprotein of Nipah virus and C-type nano...

SupramoleculeName: The complex of fusion glycoprotein of Nipah virus and C-type nanoantibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #2: Fusion glycoprotein of Nipah virus

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

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Supramolecule #3: C-type nanoantibodies targeting NiV and HeV fusion proteins

SupramoleculeName: C-type nanoantibodies targeting NiV and HeV fusion proteins
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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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: Nipah virus
Molecular weightTheoretical: 55.495438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDCVG DVRLAGVCM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVFTAL QDYINTNLVP T IDKIPCKQ ...String:
ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDCVG DVRLAGVCM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVFTAL QDYINTNLVP T IDKIPCKQ 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 DYIKEAQRLL DTVNPSMKQI EDKIEEILSK IYHIE NEIA RIKKLIGEGS GGHHHHHH

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: C-type nanoantibody

MacromoleculeName: C-type nanoantibody / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.008798 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
APSVLCLPPK PKDILMISRT PEVTCVVSDD SHSLHRVKFR WYVDGVEVHN AWTEPRDDYF NTTDRVVSKL TVLHQDWLNG KEYKCKVSA RLYGHIVPWN QGPTECTISK ANGQAGHHHH HHGDYKDDDD KG

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 12 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 226602
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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