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- EMDB-71873: Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-71873
TitleHuman respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-59
Map data
Sample
  • Complex: Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-59
    • Protein or peptide: VHH A2R3-59
    • Protein or peptide: Hemagglutinin-neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHuman respirovirus / hemagglutinin-neuraminidase / nanobody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesHuman respirovirus 3 / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhou L / Ramamohan AR / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-59
Authors: Zhou L / McLellan JS
History
DepositionJul 31, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71873.png

Downloads & links

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Map

FileDownload / File: emd_71873.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279.9 Å		0.93 Å/pix.
x 300 pix.
= 279.9 Å		0.93 Å/pix.
x 300 pix.
= 279.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.026292417 - 1.9690121
Average (Standard dev.)0.0007454154 (±0.02010524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71873_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71873_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 : Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex...

EntireName: Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-59
Components
  • Complex: Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-59
    • Protein or peptide: VHH A2R3-59
    • Protein or peptide: Hemagglutinin-neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex...

SupramoleculeName: Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-59
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human respirovirus 3

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Macromolecule #1: VHH A2R3-59

MacromoleculeName: VHH A2R3-59 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.153378 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString:
GSQVQLQESG GGLVQPGGSL RLSCAASGSI SGINGMGWYR QAPGKQRELV AAITSGGSTN YADSVKGRFT ISRDNAKNTV DLQMNSLQP EDTAVYYCYV SSTPSWGLYD DYWGQGTQVT VSSGSHHHHH HHH

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Macromolecule #2: Hemagglutinin-neuraminidase

MacromoleculeName: Hemagglutinin-neuraminidase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 55.954785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLSAWSHPQ FEKGSMKQLE DKIEELLSKI YHLENEIARL KKLIGEGAGS RITHDVGIKP LNPDDFWRC TSGLPSLMKT PKIRSMPGPG LLAMPTTVDG CVRTPSLVIN DLIYAYTSNL ITRGCQDIGK SYQVLQIGII T VNSDLVPD ...String:
MPMGSLQPLA TLYLLGMLVA SVLSAWSHPQ FEKGSMKQLE DKIEELLSKI YHLENEIARL KKLIGEGAGS RITHDVGIKP LNPDDFWRC TSGLPSLMKT PKIRSMPGPG LLAMPTTVDG CVRTPSLVIN DLIYAYTSNL ITRGCQDIGK SYQVLQIGII T VNSDLVPD LNPRISHTFN INDNRKSCSL ALLNTDVYQL CSTPKVDERS DYASSGIEDI VLDIVNYDGS ISTTRFKNNN IS FDQPYAA LYPSVGPGIY YKGKIIFLGY GGLEHPINEN AICNTTGCPG KTQRDCNQAS HSPWFSDRRM VNSIIVVDKG LNS VPKLKV WTISMRQNYW GSEGRLLLLG NKIYIYTRST SWHSKLQLGI IDITDYSDIR IKWTWHNVLS RPGNNECPWG HSCP DGCIT GVYTDAYPLN PTGSIVSSVI LDSQKSRVNP VITYSTATER VNELAIRNKT LSAGYTTTSC ITHYNKGYCF HIVEI NHKS LNTFQPMLFK TEIPKSCS

UniProtKB: Hemagglutinin-neuraminidase

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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: 4 / 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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold 3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92857
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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