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- EMDB-18993: pentameric IgMFc-AIM complex global refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-18993
Titlepentameric IgMFc-AIM complex global refinement
Map data
Sample
  • Complex: human IgM-Fc/AIM complex
    • Protein or peptide: CD5 antigen-like
    • Protein or peptide: Ig-like domain-containing protein
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsScavenger Receptor Cysteine-Rich / IgM / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of complement-dependent cytotoxicity / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding / regulation of complement activation / glomerular filtration / immunoglobulin receptor binding ...positive regulation of complement-dependent cytotoxicity / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA binding / regulation of complement activation / glomerular filtration / immunoglobulin receptor binding / positive regulation of respiratory burst / humoral immune response / immune system process / cellular defense response / Scavenging of heme from plasma / antigen binding / Cell surface interactions at the vascular wall / antibacterial humoral response / protein-containing complex assembly / protein-macromolecule adaptor activity / blood microparticle / adaptive immune response / immune response / inflammatory response / innate immune response / apoptotic process / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin J chain / Immunoglobulin J chain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / : / Immunoglobulin/major histocompatibility complex, conserved site ...Immunoglobulin J chain / Immunoglobulin J chain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / : / 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 / CD5 antigen-like / Immunoglobulin J chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsChen Q / Arai S / Miyazaki T / Rosenthal P
Funding support United Kingdom, Japan, 5 items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
Wellcome Trust United Kingdom
Japan Agency for Medical Research and Development (AMED) Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM reveals structural basis for human AIM/CD5L recognition of polymeric immunoglobulin M.
Authors: Qu Chen / Kazuhiro Ishii / Haruka Mori / Akemi Nishijima / Satoko Arai / Toru Miyazaki / Peter B Rosenthal /
Abstract: Cell surface scavenger receptors contribute to homoeostasis and the response to pathogens and products associated with damage by binding to common molecular features on a wide range of targets. ...Cell surface scavenger receptors contribute to homoeostasis and the response to pathogens and products associated with damage by binding to common molecular features on a wide range of targets. Apoptosis inhibitor of macrophage (AIM/CD5L) is a soluble protein belonging to the scavenger receptor cysteine-rich (SRCR) superfamily that contributes to prevention of a wide range of diseases associated with infection, inflammation, and cancer. AIM forms complexes with IgM pentamers which helps maintain high-levels of circulating AIM in serum for subsequent activation on release from the complex. The structural basis for AIM recognition of IgM as well as other binding targets is unknown. Here we apply cryogenic electron microscopy imaging (cryo-EM) to show how interfaces on both of AIM's C-terminal SRCR domains interact with the Fcμ constant region and J chain components of the IgM core. Both SRCR interfaces are also shown to contribute interactions important for AIM binding to damage-associated molecular patterns (DAMPs).
History
DepositionNov 28, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18993.png

Downloads & links

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Map

FileDownload / File: emd_18993.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 600 pix.
= 507.6 Å		0.85 Å/pix.
x 600 pix.
= 507.6 Å		0.85 Å/pix.
x 600 pix.
= 507.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.846 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.3663414 - 2.2380037
Average (Standard dev.)0.0004774281 (±0.02025655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 507.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18993_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_18993_additional_1.map
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Half map: #2

Fileemd_18993_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_18993_half_map_2.map
Projections & Slices
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Sample components

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Entire : human IgM-Fc/AIM complex

EntireName: human IgM-Fc/AIM complex
Components
  • Complex: human IgM-Fc/AIM complex
    • Protein or peptide: CD5 antigen-like
    • Protein or peptide: Ig-like domain-containing protein
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: human IgM-Fc/AIM complex

SupramoleculeName: human IgM-Fc/AIM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CD5 antigen-like

MacromoleculeName: CD5 antigen-like / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.10025 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: SPSGVRLVGG LHRCEGRVEV EQKGQWGTVC DDGWDIKDVA VLCRELGCGA ASGTPSGILY EPPAEKEQKV LIQSVSCTGT EDTLAQCEQ EEVYDCSHDE DAGASCENPE SSFSPVPEGV RLADGPGHCK GRVEVKHQNQ WYTVCQTGWS LRAAKVVCRQ L GCGRAVLT ...String:
SPSGVRLVGG LHRCEGRVEV EQKGQWGTVC DDGWDIKDVA VLCRELGCGA ASGTPSGILY EPPAEKEQKV LIQSVSCTGT EDTLAQCEQ EEVYDCSHDE DAGASCENPE SSFSPVPEGV RLADGPGHCK GRVEVKHQNQ WYTVCQTGWS LRAAKVVCRQ L GCGRAVLT QKRCNKHAYG RKPIWLSQMS CSGREATLQD CPSGPWGKNT CNHDEDTWVE CEDPFDLRLV GGDNLCSGRL EV LHKGVWG SVCDDNWGEK EDQVVCKQLG CGKSLSPSFR DRKCYGPGVG RIWLDNVRCS GEEQSLEQCQ HRFWGFHDCT HQE DVAVIC SG

UniProtKB: CD5 antigen-like

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Macromolecule #2: Ig-like domain-containing protein

MacromoleculeName: Ig-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.715379 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DYKDDDDKGS GSGIAELPPK VSVFVPPRDG FFGNPRKSKL ICQATGFSPR QIQVSWLREG KQVGSGVTTD QVQAEAKESG PTTYKVTST LTIKESDWLS QSMFTCRVDH RGLTFQQNAS SMCVPDQDTA IRVFAIPPSF ASIFLTKSTK LTCLVTDLTT Y DSVTISWT ...String:
DYKDDDDKGS GSGIAELPPK VSVFVPPRDG FFGNPRKSKL ICQATGFSPR QIQVSWLREG KQVGSGVTTD QVQAEAKESG PTTYKVTST LTIKESDWLS QSMFTCRVDH RGLTFQQNAS SMCVPDQDTA IRVFAIPPSF ASIFLTKSTK LTCLVTDLTT Y DSVTISWT RQNGEAVKTH TNISESHPNA TFSAVGEASI CEDDWNSGER FTCTVTHTDL PSPLKQTISR PKGVALHRPD VY LLPPARE QLNLRESATI TCLVTGFSPA DVFVQWMQRG QPLSPEKYVT SAPMPEPQAP GRYFAHSILT VSEEEWNTGE TYT CVVAHE ALPNRVTERT VDKSTGKPTL YNVSLVMSDT AGTCY

UniProtKB: Ig-like domain-containing protein

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Macromolecule #3: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.306881 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
MKNHLLFWGV LAVFIKAVHV KAQEDERIVL VDNKCKCARI TSRIIRSSED PNEDIVERNI RIIVPLNNRE NISDPTSPLR TRFVYHLSD LCKKCDPTEV ELDNQIVTAT QSNICDEDSA TETCYTYDRN KCYTAVVPLV YGGETKMVET ALTPDACYPD E QKLISEED L

UniProtKB: Immunoglobulin J chain

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / 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

Concentration1.3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 52.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8bpf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 501789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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