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- PDB-9ec7: Cryo-EM structure of avian tetrameric IgA-Fc/J chain -

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Basic information

Entry
Database: PDB / ID: 9ec7
TitleCryo-EM structure of avian tetrameric IgA-Fc/J chain
Components
  • Immunoglobulin heavy chain alpha
  • Joining chain of multimeric IgA and IgM
KeywordsIMMUNE SYSTEM / SECRETORY IMMUNOGLOBULIN A / ANTIBODY / ANAS PLATYRHYNCHOS
Function / homology
Function and homology information


pentameric IgM immunoglobulin complex / immunoglobulin receptor binding / humoral immune response
Similarity search - Function
Immunoglobulin J chain / Immunoglobulin J chain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin J chain / Immunoglobulin J chain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Ig-like domain-containing protein / Joining chain of multimeric IgA and IgM
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsSchneider, R.M. / Stadtmueller, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Avian Immunoglobulin A: Structure-function relationships unique to birds guide understanding of host protection against pathogens
Authors: Schneider, R.M. / Liu, Q. / Stadtmueller, B.M.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 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: Immunoglobulin heavy chain alpha
B: Immunoglobulin heavy chain alpha
C: Immunoglobulin heavy chain alpha
D: Immunoglobulin heavy chain alpha
E: Immunoglobulin heavy chain alpha
F: Immunoglobulin heavy chain alpha
G: Immunoglobulin heavy chain alpha
H: Immunoglobulin heavy chain alpha
J: Joining chain of multimeric IgA and IgM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,95616
Polymers315,0139
Non-polymers3,9447
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody
Immunoglobulin heavy chain alpha


Mass: 37401.484 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Details (production host): pD2610-v1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A0A8B9SH23
#2: Protein Joining chain of multimeric IgA and IgM


Mass: 15800.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: JCHAIN / Details (production host): pD2610-v1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A0A8B9TFQ9
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
Has ligand of interestN
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: Avian tetrameric IgA-Fc/J / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Anas platyrhynchos (mallard)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F / Plasmid: pD2610-v1
Buffer solutionpH: 7.4 / Details: tris buffered saline
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Three applications of 3 uL of sample at 0.1 mg/mL were applied to each grid at 4C and 100% relative humidity. Each application was followed by a 3 s wait and 2 s blot time. After the third ...Details: Three applications of 3 uL of sample at 0.1 mg/mL were applied to each grid at 4C and 100% relative humidity. Each application was followed by a 3 s wait and 2 s blot time. After the third blot, the grid was vitrified.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 81000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.21 sec. / Electron dose: 57.79 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5559
Details: 2544 movies collected with untitled stage and 3015 movies collected with 30 degree tilted stage.

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2EPUimage acquisitioncollection with untitled stage
3Leginonimage acquisitioncollection with tilted stage
5cryoSPARCCTF correction
8Coot0.9.8.1model fitting
10PHENIX1.20.1_4487model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 320667 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingDetails: trRosetta / Source name: Other / Type: in silico model

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