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- EMDB-45622: Fab fragment of Antibody with NiV glycoprotein F -

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Basic information

Entry
Database: EMDB / ID: EMD-45622
TitleFab fragment of Antibody with NiV glycoprotein F
Map dataFile exported as .mrc at contour 0.18 and pixel spacing 0.825 from session. Sharpened map using DeepEMhancer
Sample
  • Complex: Fab fragment with NiV F0 fusion protein
    • Protein or peptide: Antibody Heavy Chain
    • Protein or peptide: Antibody Light Chain
    • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFusion complex antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol
Similarity search - Function
Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
Thymidylate synthase
Similarity search - Component
Biological speciesHenipavirus nipahense / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsOuizougun-Oubari M / Bajic G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Broadly neutralizing antibody in complex with Nipah fusion glycoprotein
Authors: Bajic G / Ouizougun-Oubari M
History
DepositionJul 3, 2024-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45622.png

Downloads & links

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Map

FileDownload / File: emd_45622.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFile exported as .mrc at contour 0.18 and pixel spacing 0.825 from session. Sharpened map using DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 334 pix.
= 275.55 Å		0.83 Å/pix.
x 334 pix.
= 275.55 Å		0.83 Å/pix.
x 334 pix.
= 275.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.0017820997 - 1.6687081
Average (Standard dev.)0.0021097327 (±0.03189735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 275.55 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: File exported as .mrc at contour 0.18 and...

Fileemd_45622_additional_1.map
AnnotationFile exported as .mrc at contour 0.18 and pixel spacing 0.825 from session
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map half A cont 0.18

Fileemd_45622_half_map_1.map
AnnotationMap_half_A cont 0.18
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map half B cont 0.18

Fileemd_45622_half_map_2.map
AnnotationMap_half_B cont 0.18
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fab fragment with NiV F0 fusion protein

EntireName: Fab fragment with NiV F0 fusion protein
Components
  • Complex: Fab fragment with NiV F0 fusion protein
    • Protein or peptide: Antibody Heavy Chain
    • Protein or peptide: Antibody Light Chain
    • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Fab fragment with NiV F0 fusion protein

SupramoleculeName: Fab fragment with NiV F0 fusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
Source (natural)Organism: Henipavirus nipahense

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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: 60.666555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GGILHYEKLS KIGLVKGVTR KYKIKSNPLT KDIVIKMIPN VSNMSQCTGS VMENYKTRL NGILTPIKGA LEIYKNNTHD CVGDVRLAGV CMAGVAIGIA TAAQITAGVA LYEAMKNADN INKLKSSIES T NEAVVKLQ ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GGILHYEKLS KIGLVKGVTR KYKIKSNPLT KDIVIKMIPN VSNMSQCTGS VMENYKTRL NGILTPIKGA LEIYKNNTHD CVGDVRLAGV CMAGVAIGIA TAAQITAGVA LYEAMKNADN INKLKSSIES T NEAVVKLQ ETAEKTVYVF TALQDYINTN LVPTIDKIPC KQTELSLDLA LSKYLSDLLF VFGPNLQDPV SNSMTIQAIS QA FGGNYET LLRTLGYATE DFDDLLESDS ITGQIIYVDL SSYYIIVRVY FPILTEIQQA YIQELLPVSF NNDNSEWISI VPN FILVRN TLISNIEIGF CLITKRSVIC NQDYATPMTN NMRECLTGST EKCPRELVVS SHVPRFALSN GVLFANCISV TCQC QTTGR AISQSGEQTL LMIDNTTCPT AVLGNVIISL GKYLGSVNYN SEGIAIGPPV FTDKVDISSQ ISSMNQSLQQ SKDYI KEAQ RLLDGTMKQI EDKIEEILSK IYHIENEIAR IKKLIGEGGS GGSGLNDIFE AQKIEWHEGR TKHHHHHH

UniProtKB: Thymidylate synthase

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Macromolecule #2: Antibody Heavy Chain

MacromoleculeName: Antibody Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.464017 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYGIHWVRQA PGKGLEWVAL IDYAGSNKYY SDSVKGRFTI SRDNSKNTLY LQMKSLRAE DTAVYYCARD RDYGILTGYP DYWGQGALVT VSS

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Macromolecule #3: Antibody Light Chain

MacromoleculeName: Antibody Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.568906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IVLTQSPATL SLSPGERATL SCRASQSVSS YLAWYQQKPG QAPRLLIYDA SNRATGIPAR FSGSGSGTDF TLTISSLEPE DFAVYYCQH RSNWPPLTFG GGTKVEIK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 135929
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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