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- EMDB-47901: Cryo-EM structure of avian tetrameric IgA-Fc/J chain -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47901
TitleCryo-EM structure of avian tetrameric IgA-Fc/J chain
Map data
Sample
  • Complex: Avian tetrameric IgA-Fc/J
    • Protein or peptide: Immunoglobulin heavy chain alpha
    • Protein or peptide: Joining chain of multimeric IgA and IgM
KeywordsSECRETORY IMMUNOGLOBULIN A / ANTIBODY / ANAS PLATYRHYNCHOS / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsSchneider RM / Liu Q / Stadtmueller BM
Funding support United States, 1 items
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 RM / Liu Q / Stadtmueller BM
History
DepositionNov 13, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47901.png

Downloads & links

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Map

FileDownload / File: emd_47901.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 440 pix.
= 463.76 Å		1.05 Å/pix.
x 440 pix.
= 463.76 Å		1.05 Å/pix.
x 440 pix.
= 463.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.22786255 - 0.650397
Average (Standard dev.)0.000005422504 (±0.0098662125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 463.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47901_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_47901_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 : Avian tetrameric IgA-Fc/J

EntireName: Avian tetrameric IgA-Fc/J
Components
  • Complex: Avian tetrameric IgA-Fc/J
    • Protein or peptide: Immunoglobulin heavy chain alpha
    • Protein or peptide: Joining chain of multimeric IgA and IgM

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Supramolecule #1: Avian tetrameric IgA-Fc/J

SupramoleculeName: Avian tetrameric IgA-Fc/J / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Anas platyrhynchos (mallard)

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Macromolecule #1: Immunoglobulin heavy chain alpha

MacromoleculeName: Immunoglobulin heavy chain alpha / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Anas platyrhynchos (mallard)
Molecular weightTheoretical: 37.401484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHGSIP TVKLLSYPTQ EDPENRVLLV CLIEGLQGSN AQVEWLINQQ VQELEEDNYS CSECSNKKAT QWSQVNVSRQ SWDQGAEFS CRVSHTSLKE PIVESISTYC TSAGPKLEVT LLPPSLEDLY ISQNASVTCV ATNAPQDLKF SWSRSEGTAL D VVTGEPQK ...String:
HHHHHHGSIP TVKLLSYPTQ EDPENRVLLV CLIEGLQGSN AQVEWLINQQ VQELEEDNYS CSECSNKKAT QWSQVNVSRQ SWDQGAEFS CRVSHTSLKE PIVESISTYC TSAGPKLEVT LLPPSLEDLY ISQNASVTCV ATNAPQDLKF SWSRSEGTAL D VVTGEPQK QENGLYRLTS VLKICAEEWN SGESFTCGVA GPEIQGSVTK SVQKDLAVSV QAPSVYVFPP PAEELARQET AT LTCLASG FRPRDILVTW TQQDRPVASG SFSTFGPQEG EAGLFSVYSK LSVAAAEWQR GDVFACVVGH DGIPLNFVQK SLD KSTGKP TQVNVSVVLS DADSTCY

UniProtKB: Ig-like domain-containing protein

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Macromolecule #2: Joining chain of multimeric IgA and IgM

MacromoleculeName: Joining chain of multimeric IgA and IgM / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anas platyrhynchos (mallard)
Molecular weightTheoretical: 15.800736 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TLLDYDGEER VLVNNKCKCT TVTSRLVPSK ENPDEEILER NIRITVPLRS RQNISDPTSP LRTTFVYRMA ELCKKCDPVE VELGGEIYE AQQSTSCNEP ETCYTYNRDK CYTTTFPFIY HGETKHIQAA LTPASCYAD

UniProtKB: Joining chain of multimeric IgA and IgM

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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

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: tris buffered saline
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThree 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5559 / Average exposure time: 3.21 sec. / Average electron dose: 57.79 e/Å2
Details: 2544 movies collected with untitled stage and 3015 movies collected with 30 degree tilted stage.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 320667
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: trRosetta
RefinementSpace: REAL
Output model

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

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