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- EMDB-22309: Dimeric Immunoglobin A (dIgA) -

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Basic information

Entry
Database: EMDB / ID: EMD-22309
TitleDimeric Immunoglobin A (dIgA)
Map dataMain map, sharpened - 3.3A
Sample
  • Complex: Secretory Immunoglobin A
    • Protein or peptide: Igh protein
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


Scavenging of heme from plasma / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding / Cell surface interactions at the vascular wall / glomerular filtration / phosphatidylcholine binding ...Scavenging of heme from plasma / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding / Cell surface interactions at the vascular wall / glomerular filtration / phosphatidylcholine binding / peptidoglycan binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of respiratory burst / humoral immune response / complement activation, classical pathway / antigen binding / antibacterial humoral response / single-stranded DNA binding / protein-macromolecule adaptor activity / protein-containing complex assembly / adaptive immune response / innate immune response / protein homodimerization activity
Similarity search - Function
Immunoglobulin J chain / Immunoglobulin J chain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...Immunoglobulin J chain / Immunoglobulin J chain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Immunoglobulin J chain / Ig alpha chain C region / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKumar Bharathkar S / Parker BP
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM10460 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI041239 United States
CitationJournal: Elife / Year: 2020
Title: The structures of secretory and dimeric immunoglobulin A.
Authors: Sonya Kumar Bharathkar / Benjamin W Parker / Andrey G Malyutin / Nandan Haloi / Kathryn E Huey-Tubman / Emad Tajkhorshid / Beth M Stadtmueller /
Abstract: Secretory (S) Immunoglobulin (Ig) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that ...Secretory (S) Immunoglobulin (Ig) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that assemble with one joining-chain (JC) to form dimeric (d) IgA that is bound by the polymeric Ig-receptor ectodomain, called secretory component (SC). Here, we report the cryo-electron microscopy structures of murine SIgA and dIgA. Structures reveal two IgAs conjoined through four heavy-chain tailpieces and the JC that together form a β-sandwich-like fold. The two IgAs are bent and tilted with respect to each other, forming distinct concave and convex surfaces. In SIgA, SC is bound to one face, asymmetrically contacting both IgAs and JC. The bent and tilted arrangement of complex components limits the possible positions of both sets of antigen-binding fragments (Fabs) and preserves steric accessibility to receptor-binding sites, likely influencing antigen binding and effector functions.
History
DepositionJul 18, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.277
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.277
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jg1
  • Surface level: 0.277
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22309.png

Downloads & links

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Map

FileDownload / File: emd_22309.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, sharpened - 3.3A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.277 / Movie #1: 0.277
Minimum - Maximum-1.4215939 - 2.347467
Average (Standard dev.)0.0000061173164 (±0.040114682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8360.8360.836
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z300.960300.960300.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.4222.3470.000

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Supplemental data

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Mask #1

Fileemd_22309_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Main map, unsharpened.

Fileemd_22309_additional_1.map
AnnotationMain map, unsharpened.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: dIgA half-map 1 from Non-Uniform Refinement job in CS2

Fileemd_22309_half_map_1.map
AnnotationdIgA half-map 1 from Non-Uniform Refinement job in CS2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: dIgA half-map 1 from Non-Uniform Refinement job in CS2

Fileemd_22309_half_map_2.map
AnnotationdIgA half-map 1 from Non-Uniform Refinement job in CS2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Secretory Immunoglobin A

EntireName: Secretory Immunoglobin A
Components
  • Complex: Secretory Immunoglobin A
    • Protein or peptide: Igh protein
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Secretory Immunoglobin A

SupramoleculeName: Secretory Immunoglobin A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Igh protein

MacromoleculeName: Igh protein / type: protein_or_peptide / ID: 1
Details: Genes encoding the mus musculus IgA HC constant region and the lambda LC constant region were fused with HC and LC variable region sequences to create complete HC and LC sequences. The HC ...Details: Genes encoding the mus musculus IgA HC constant region and the lambda LC constant region were fused with HC and LC variable region sequences to create complete HC and LC sequences. The HC and LC variable region is not modeled in this structure. Since authors have chosen not to provide complete sample sequence of the HC and LC variable region, the UNKs were not included in the sequence.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 37.976891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WGQGTLVTVS AESARNPTIY PLTLPPALSS DPVIIGCLIH DYFPSGTMNV TWGKSGKDIT TVNFPPALAS GGRYTMSSQL TLPAVECPE GESVKCSVQH DSNPVQELDV NCSGPTPPPP ITIPSCQPSL SLQRPALEDL LLGSDASITC TLNGLRNPEG A VFTWEPST ...String:
WGQGTLVTVS AESARNPTIY PLTLPPALSS DPVIIGCLIH DYFPSGTMNV TWGKSGKDIT TVNFPPALAS GGRYTMSSQL TLPAVECPE GESVKCSVQH DSNPVQELDV NCSGPTPPPP ITIPSCQPSL SLQRPALEDL LLGSDASITC TLNGLRNPEG A VFTWEPST GKDAVQKKAV QNSCGCYSVS SVLPGCAERW NSGASFKCTV THPESGTLTG TIAKVTVNTF PPQVHLLPPP SE ELALNEL LSLTCLVRAF NPKEVLVRWL HGNEELSPES YLVFEPLKEP GEGATTYLVT SVLRVSAETW KQGDQYSCMV GHE ALPMNF TQKTIDRLSG KPTNVSVSVI MSEGDGICY

UniProtKB: Igh protein

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Macromolecule #2: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.637499 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DDEATILADN KCMCTRVTSR IIPSTEDPNE DIVERNIRIV VPLNNRENIS DPTSPLRRNF VYHLSDVCKK CDPVEVELED QVVTATQSN ICNEDDGVPE TCYMYDRNKC YTTMVPLRYH GETKMVQAAL TPDSCYPD

UniProtKB: Immunoglobulin J chain

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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: 2 / 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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time - 0s Drain time - 0s Blot time - 6s Blot Force - 5.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 59808 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsSuper resolution images were collected. During motion correction, movies were binned by 2.
Particle selectionNumber selected: 1808799
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 288823
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.12)
FSC plot (resolution estimation)

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