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- EMDB-63997: The structure of Myanmar_N2 and AS4C_Fab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63997
TitleThe structure of Myanmar_N2 and AS4C_Fab complex
Map data
Sample
  • Complex: The structure of Myanmar_N2 and AS4C_Fab complex
    • Protein or peptide: AS4C antibody lignt chain
    • Protein or peptide: AS4C antibody heavy chain
    • Protein or peptide: Vasodilator-stimulated phosphoprotein,Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
Keywordsprotein / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / exo-alpha-sialidase / positive regulation of actin filament polymerization / exo-alpha-sialidase activity / lamellipodium membrane / Generation of second messenger molecules ...profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / exo-alpha-sialidase / positive regulation of actin filament polymerization / exo-alpha-sialidase activity / lamellipodium membrane / Generation of second messenger molecules / bicellular tight junction / axon guidance / viral budding from plasma membrane / neural tube closure / SH3 domain binding / actin cytoskeleton / actin binding / carbohydrate metabolic process / protein homotetramerization / postsynapse / cadherin binding / focal adhesion / host cell plasma membrane / virion membrane / glutamatergic synapse / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 ...Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Neuraminidase / Vasodilator-stimulated phosphoprotein
Similarity search - Component
Biological speciesInfluenza A virus (A/California/VRDL364/2009(mixed)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsSun JQ / Yang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: To Be Published
Title: The structure of Myanmar_N2 and AS4C_Fab complex
Authors: Sun JQ / Yang H
History
DepositionApr 1, 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_63997.png

Downloads & links

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Map

FileDownload / File: emd_63997.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 460 pix.
= 391. Å		0.85 Å/pix.
x 460 pix.
= 391. Å		0.85 Å/pix.
x 460 pix.
= 391. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.228
Minimum - Maximum-0.15197451 - 1.0135559
Average (Standard dev.)-0.000021421516 (±0.030225588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 391.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63997_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_63997_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 structure of Myanmar_N2 and AS4C_Fab complex

EntireName: The structure of Myanmar_N2 and AS4C_Fab complex
Components
  • Complex: The structure of Myanmar_N2 and AS4C_Fab complex
    • Protein or peptide: AS4C antibody lignt chain
    • Protein or peptide: AS4C antibody heavy chain
    • Protein or peptide: Vasodilator-stimulated phosphoprotein,Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: The structure of Myanmar_N2 and AS4C_Fab complex

SupramoleculeName: The structure of Myanmar_N2 and AS4C_Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/California/VRDL364/2009(mixed))

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Macromolecule #1: AS4C antibody lignt chain

MacromoleculeName: AS4C antibody lignt chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.697562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGVTFS DHAMNWVRQA PGKGLEWVAG IIGSGGNTKY ADSVKGRFTI SRDNSENTVH LQMNSLRAE DTAMYYCAKT AHTSGHFYNG MDVWGLGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EVQLVESGGG LVQPGGSLRL SCAASGVTFS DHAMNWVRQA PGKGLEWVAG IIGSGGNTKY ADSVKGRFTI SRDNSENTVH LQMNSLRAE DTAMYYCAKT AHTSGHFYNG MDVWGLGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPKSCDK HHHHHH

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Macromolecule #2: AS4C antibody heavy chain

MacromoleculeName: AS4C antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.469979 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCQASQDIA NYLSWYQQKP GKAPKLLIYD AANLERGVPS RFSGSGSGTD FTFTISSLLP EDFATYYCQ QYDSVPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCQASQDIA NYLSWYQQKP GKAPKLLIYD AANLERGVPS RFSGSGSGTD FTFTISSLLP EDFATYYCQ QYDSVPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGECS

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Macromolecule #3: Vasodilator-stimulated phosphoprotein,Neuraminidase

MacromoleculeName: Vasodilator-stimulated phosphoprotein,Neuraminidase / type: protein_or_peptide / ID: 3
Details: Sequence reference for strain 'Influenza A virus (A/California/VRDL364/2009(mixed))' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id C3PQB5.
Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus (A/California/VRDL364/2009(mixed))
Molecular weightTheoretical: 54.392961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PHHHHHHSSS DYSDLQRVKQ ELLEEVKKEL QKVKEEIIEA FVQELRKRG SLVPRGSPSR SEFEYRNWSK PQCDITGFAP FSKDNSIRLS AGGDIWVTRE PYVSCDPDKC YQFALGKGTT L NNVHSNNT ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PHHHHHHSSS DYSDLQRVKQ ELLEEVKKEL QKVKEEIIEA FVQELRKRG SLVPRGSPSR SEFEYRNWSK PQCDITGFAP FSKDNSIRLS AGGDIWVTRE PYVSCDPDKC YQFALGKGTT L NNVHSNNT VRDRTPYRTL LMNELGVPFH LGTKQVCIAW SSSSCHDGKA WLHVCITGDD KNATASFIYN GRLVDSVVSW SK EILRTQE SECVCINGTC TVVMTDGSAS GKADTKILFI EEGKIVHTST LSGSAQHVEE CSCYPRYPGV RCVCRDNWKG SNR PIVDIN IKDHSIVSSY VCSGLVGDTP RKNDSSSSSH CLDPNNEEGG HGVKGWAFDD GNDVWMGRTI SEKSRLGYET FKVI EGWSN PKSKLQINRQ VIVDRGNRSG YSGIFSVEGK SCINRCFYVE LIRGRKEETE VLWTSNSIVV FCGTSGTYGT GSWPD GADI NLMPI

UniProtKB: Vasodilator-stimulated phosphoprotein, Neuraminidase

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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 KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 217243
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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