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- EMDB-49948: Cryo-EM structure of antibody 22F5 in complex with pre-fusion sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-49948
TitleCryo-EM structure of antibody 22F5 in complex with pre-fusion stabilized LayV-F
Map data
Sample
  • Complex: 22F5 Antibody Fab bound to pre-fusion stabilized Langya virus fusion protein
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Antibody 22F5 Heavy Chain
    • Protein or peptide: Antibody 22F5 Kappa Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLangya virus / parahenipavirus / cross-reactive / DII domain / ANTIVIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homologyPrecursor 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 speciesLangya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsMay AJ / Kumar U / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: Structural and antigenic characterization of novel and diverse Henipavirus glycoproteins.
Authors: May AJ / Lella M / Lindenberger J / Berkman A / Kumar U / Dutta M / Barr M / Parks R / Lu X / Berry M / Newman A / Huang X / Song K / Ilevbare V / Sammour S / Park CS / Adhikari RD / Devkota ...Authors: May AJ / Lella M / Lindenberger J / Berkman A / Kumar U / Dutta M / Barr M / Parks R / Lu X / Berry M / Newman A / Huang X / Song K / Ilevbare V / Sammour S / Park CS / Adhikari RD / Devkota P / Janowska K / Liu Y / Scapellato G / Spence TN / Mansouri K / Wiehe K / Edwards RJ / Saunders KO / Haynes BF / Acharya P
History
DepositionMar 31, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49948.png

Downloads & links

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Map

FileDownload / File: emd_49948.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 256 pix.
= 384. Å		1.5 Å/pix.
x 256 pix.
= 384. Å		1.5 Å/pix.
x 256 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.324
Minimum - Maximum-1.1483903 - 1.636969
Average (Standard dev.)0.000031079857 (±0.04062224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49948_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_49948_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 : 22F5 Antibody Fab bound to pre-fusion stabilized Langya virus fus...

EntireName: 22F5 Antibody Fab bound to pre-fusion stabilized Langya virus fusion protein
Components
  • Complex: 22F5 Antibody Fab bound to pre-fusion stabilized Langya virus fusion protein
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Antibody 22F5 Heavy Chain
    • Protein or peptide: Antibody 22F5 Kappa Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 22F5 Antibody Fab bound to pre-fusion stabilized Langya virus fus...

SupramoleculeName: 22F5 Antibody Fab bound to pre-fusion stabilized Langya virus fusion protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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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: Langya virus
Molecular weightTheoretical: 61.504918 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLAL NAMLDNVKSC NNKYRFAGAC MAGVALGVAT AATVTAGIAL HRSNENAQAI ANMKNAIQNT NEAVKQLQLA N KQTLAVID ...String:
MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLAL NAMLDNVKSC NNKYRFAGAC MAGVALGVAT AATVTAGIAL HRSNENAQAI ANMKNAIQNT NEAVKQLQLA N KQTLAVID TIRGEINNNI IPVINQLSCD TIGLSVGIKL TQYYSEILTA FGPALQNPVN TRITIQAISS VFNRNFDELL KI MGYTSGD LYEILHSGLI RGNIIDVDVE AGYIALEIEF PNLTLVPNAV VQELMPISYN VDGDEWVTLV PRFVLTRTTL LSN IDTSRC TVTESSVICD NDYALPMSYE LIGCLQGDTS KCAREKVVSS YVPRFALSDG LVYANCLNTI CRCMDTDTPI SQSL GTTVS LLDNKKCLVY QVGDILISVG SYLGEGEYSA DNVELGPPVV IDKIDIGNQL AGINQTLQNA EDYIEKSEEF LKGIN PSIG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGR SLEVLFQGPG HHHHHHHHSA WSHPQFEKGG GSGGGGSGGS AWSHPQ FEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Antibody 22F5 Heavy Chain

MacromoleculeName: Antibody 22F5 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.19598 KDa
SequenceString: QLVQSGAEVK KPGASVKVSC KASGYTFTGY YMHWVRQAPG QGLEWMGWIN PNNGGRNYVQ KFQGRVTMTR DTSISTAYME LSSLSSDDT AVYYCARAGT SDWYFDLWGR GTLVTVSSAS TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH ...String:
QLVQSGAEVK KPGASVKVSC KASGYTFTGY YMHWVRQAPG QGLEWMGWIN PNNGGRNYVQ KFQGRVTMTR DTSISTAYME LSSLSSDDT AVYYCARAGT SDWYFDLWGR GTLVTVSSAS TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH TFPAVLQSDL YTLSSSVTVP SSTWPSQTVT CNVAHPASST KVDKKIVP

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Macromolecule #3: Antibody 22F5 Kappa Light Chain

MacromoleculeName: Antibody 22F5 Kappa Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.323928 KDa
SequenceString: DIVITQSPSS LAVSVGEKVT MSCKSSQSLL NSRTRRNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDL AVYYCKQSYN SWTFGGGTKL EIKRTDAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DIVITQSPSS LAVSVGEKVT MSCKSSQSLL NSRTRRNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDL AVYYCKQSYN SWTFGGGTKL EIKRTDAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRNE C

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 30.72 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 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: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 245019
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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