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- PDB-9uax: The structure of Myanmar_N2 and AS4C_Fab complex -

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Basic information

Entry
Database: PDB / ID: 9uax
TitleThe structure of Myanmar_N2 and AS4C_Fab complex
Components
  • (AS4C antibody ...) x 2
  • Vasodilator-stimulated phosphoprotein,Neuraminidase
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / protein / 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 speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsSun, J.Q. / Yang, H.
Funding support China, 1items
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, J.Q. / Yang, H.
History
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AS4C antibody lignt chain
B: AS4C antibody heavy chain
C: AS4C antibody lignt chain
D: AS4C antibody heavy chain
E: AS4C antibody lignt chain
F: AS4C antibody heavy chain
G: AS4C antibody lignt chain
H: AS4C antibody heavy chain
I: Vasodilator-stimulated phosphoprotein,Neuraminidase
J: Vasodilator-stimulated phosphoprotein,Neuraminidase
K: Vasodilator-stimulated phosphoprotein,Neuraminidase
L: Vasodilator-stimulated phosphoprotein,Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,87624
Polymers410,24212
Non-polymers6,63412
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
AS4C antibody lignt chain


Mass: 24697.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
AS4C antibody heavy chain


Mass: 23469.979 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 8 molecules IJKL

#3: Protein
Vasodilator-stimulated phosphoprotein,Neuraminidase / VASP


Mass: 54392.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Influenza A virus (A/California/VRDL364/2009(mixed))
Gene: VASP, NA / Production host: Homo sapiens (human)
References: UniProt: P50552, UniProt: C3PQB5, exo-alpha-sialidase
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 2 types, 8 molecules

#4: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The structure of Myanmar_N2 and AS4C_Fab complex / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Influenza A virus (A/California/VRDL364/2009(mixed))
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217243 / Symmetry type: POINT
RefinementHighest resolution: 2.71 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01126180
ELECTRON MICROSCOPYf_angle_d0.74635552
ELECTRON MICROSCOPYf_dihedral_angle_d5.4673864
ELECTRON MICROSCOPYf_chiral_restr0.0534056
ELECTRON MICROSCOPYf_plane_restr0.0064540

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