[English] 日本語
Yorodumi
- EMDB-22310: Secretory Immunoglobin A (SIgA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22310
TitleSecretory Immunoglobin A (SIgA)
Map datasIgA map from CS2 non uniform refinement, sharpened - 3.3A
Sample
  • Complex: Secretory Immunoglobin A
    • Protein or peptide: Igh protein
    • Protein or peptide: Polymeric immunoglobulin receptor
    • 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 / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding ...Scavenging of heme from plasma / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / 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 / detection of chemical stimulus involved in sensory perception of bitter taste / glomerular filtration / phosphatidylcholine binding / peptidoglycan binding / receptor clustering / epidermal growth factor receptor binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of respiratory burst / humoral immune response / complement activation, classical pathway / antigen binding / Neutrophil degranulation / epidermal growth factor receptor signaling pathway / recycling endosome membrane / antibacterial humoral response / single-stranded DNA binding / protein-macromolecule adaptor activity / protein-containing complex assembly / adaptive immune response / receptor complex / innate immune response / protein homodimerization activity / plasma membrane
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 ...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
Polymeric immunoglobulin receptor / 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 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.049
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.049
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jg2
  • Surface level: 0.049
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22310.png

Downloads & links

-
Map

FileDownload / File: emd_22310.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationsIgA map from CS2 non uniform refinement, sharpened - 3.3A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 260.8 Å		0.65 Å/pix.
x 400 pix.
= 260.8 Å		0.65 Å/pix.
x 400 pix.
= 260.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.049 / Movie #1: 0.049
Minimum - Maximum-0.33150664 - 0.46019074
Average (Standard dev.)-0.000031586962 (±0.009826097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 260.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6520.6520.652
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z260.800260.800260.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3320.460-0.000

-
Supplemental data

-
Mask #1

Fileemd_22310_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sIgA EM map generated by Relion 3.X. Same...

Fileemd_22310_additional_1.map
AnnotationsIgA EM map generated by Relion 3.X. Same dataset as used with cryoSparc2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half 1 map for sIgA Relion refinement

Fileemd_22310_additional_2.map
AnnotationHalf_1 map for sIgA Relion refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half 2 map for sIgA Relion refinement

Fileemd_22310_additional_3.map
AnnotationHalf_2 map for sIgA Relion refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Mask used in Relion post-processing

Fileemd_22310_additional_4.map
AnnotationMask used in Relion post-processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sIgA map from CS2 non uniform refinement, unsharpened

Fileemd_22310_additional_5.map
AnnotationsIgA map from CS2 non uniform refinement, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half 2 map for sIgA Non-uniform refinement job

Fileemd_22310_half_map_1.map
AnnotationHalf_2 map for sIgA Non-uniform refinement job
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half 1 map for sIgA Non-uniform refinement job

Fileemd_22310_half_map_2.map
AnnotationHalf_1 map for sIgA Non-uniform refinement job
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Secretory Immunoglobin A

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

-
Supramolecule #1: Secretory Immunoglobin A

SupramoleculeName: Secretory Immunoglobin A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

-
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

-
Macromolecule #2: Polymeric immunoglobulin receptor

MacromoleculeName: Polymeric immunoglobulin receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 61.257211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KSPIFGPQEV SSIEGDSVSI TCYYPDTSVN RHTRKYWCRQ GASGMCTTLI SSNGYLSKEY SGRANLINFP ENNTFVINIE QLTQDDTGS YKCGLGTSNR GLSFDVSLEV SQVPELPSDT HVYTKDIGRN VTIECPFKRE NAPSKKSLCK KTNQSCELVI D STEKVNPS ...String:
KSPIFGPQEV SSIEGDSVSI TCYYPDTSVN RHTRKYWCRQ GASGMCTTLI SSNGYLSKEY SGRANLINFP ENNTFVINIE QLTQDDTGS YKCGLGTSNR GLSFDVSLEV SQVPELPSDT HVYTKDIGRN VTIECPFKRE NAPSKKSLCK KTNQSCELVI D STEKVNPS YIGRAKLFMK GTDLTVFYVN ISHLTHNDAG LYICQAGEGP SADKKNVDLQ VLAPEPELLY KDLRSSVTFE CD LGREVAN EAKYLCRMNK ETCDVIINTL GKRDPDFEGR ILITPKDDNG RFSVLITGLR KEDAGHYQCG AHSSGLPQEG WPI QTWQLF VNEESTIPNR RSVVKGVTGG SVAIACPYNP KESSSLKYWC RWEGDGNGHC PVLVGTQAQV QEEYEGRLAL FDQP GNGTY TVILNQLTTE DAGFYWCLTN GDSRWRTTIE LQVAEATREP NLEVTPQNAT AVLGETFTVS CHYPCKFYSQ EKYWC KWSN KGCHILPSHD EGARQSSVSC DQSSQLVSMT LNPVSKEDEG WYWCGVKQGQ TYGETTAIYI AVEER

UniProtKB: Polymeric immunoglobulin receptor

-
Macromolecule #3: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: Pelco easiGlow - 20 mA current
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.

-
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: 76687 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsSuper resolution images were collected. During motion correction, movies were binned by 2.
Particle selectionNumber selected: 956981
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 229252
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more