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- EMDB-13921: Cryo-EM structure of full-length human immunoglobulin M -

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Basic information

Entry
Database: EMDB / ID: EMD-13921
TitleCryo-EM structure of full-length human immunoglobulin M
Map data
Sample
  • Complex: Full-length human IgM pentamer
    • Protein or peptide: J chain
    • Protein or peptide: human IgM heavy chain
    • Protein or peptide: human IgM light chain
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsChen Q / Rosenthal P / Tolar P
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Cancer Research UKFC001143 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
Cancer Research UKFC001185 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001185 United Kingdom
Wellcome TrustFC001185 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Cryomicroscopy reveals the structural basis for a flexible hinge motion in the immunoglobulin M pentamer.
Authors: Qu Chen / Rajesh Menon / Lesley J Calder / Pavel Tolar / Peter B Rosenthal /
Abstract: Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure ...Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure of the human full-length IgM pentamer, revealing antigen binding domains flexibly attached to the asymmetric and rigid core formed by the Cμ4 and Cμ3 constant regions and the J-chain. A hinge is located at the Cμ3/Cμ2 domain interface, allowing Fabs and Cμ2 to pivot as a unit both in-plane and out-of-plane. This motion is different from that observed in IgG and IgA, where the two Fab arms are able to swing independently. A biased orientation of one pair of Fab arms results from asymmetry in the constant domain (Cμ3) at the IgM subunit interacting most extensively with the J-chain. This may influence the multi-valent binding to surface-associated antigens and complement pathway activation. By comparison, the structure of the Fc fragment in the IgM monomer is similar to that of the pentamer, but is more dynamic in the Cμ4 domain.
History
DepositionNov 27, 2021-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13921.png

Downloads & links

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Map

FileDownload / File: emd_13921.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.8913603 - 3.7186232
Average (Standard dev.)-3.347166e-05 (±0.038307793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 654.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13921_msk_1.map
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Additional map: #1

Fileemd_13921_additional_1.map
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Half map: #1

Fileemd_13921_half_map_1.map
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Half map: #2

Fileemd_13921_half_map_2.map
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Sample components

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Entire : Full-length human IgM pentamer

EntireName: Full-length human IgM pentamer
Components
  • Complex: Full-length human IgM pentamer
    • Protein or peptide: J chain
    • Protein or peptide: human IgM heavy chain
    • Protein or peptide: human IgM light chain

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Supramolecule #1: Full-length human IgM pentamer

SupramoleculeName: Full-length human IgM pentamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: J chain

MacromoleculeName: J chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
QEDERIVLVD NKCKCARITS RIIRSSEDPN EDIVERNIRI IVPLNNRENI SDPTSPLRTR FVYHLSDLCK KCDPTEVELD NQIVTATQSN ICDEDSATET CYTYDRNKCY TAVVPLVYGG ETKMVETALT PDACY

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Macromolecule #2: human IgM heavy chain

MacromoleculeName: human IgM heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: QVTLKESGPT LVKPTQTLTL TCTFSGFSLT TTGEGVGWIR QPPGKALEFL AFIYWNDAKR YNPSLQSRLT ITKDASKKQV VLTLTNLDPV DTATYYCART SGWDIEFEYW GQGTLVTVSS GSASAPTLFP LVSCENSPSD TSSVAVGCLA QDFLPDSITF SWKYKNNSDI ...String:
QVTLKESGPT LVKPTQTLTL TCTFSGFSLT TTGEGVGWIR QPPGKALEFL AFIYWNDAKR YNPSLQSRLT ITKDASKKQV VLTLTNLDPV DTATYYCART SGWDIEFEYW GQGTLVTVSS GSASAPTLFP LVSCENSPSD TSSVAVGCLA QDFLPDSITF SWKYKNNSDI SSTRGFPSVL RGGKYAATSQ VLLPSKDVMQ GTDEHVVCKV QHPNGNKEKN VPLPVIAELP PKVSVFVPPR DGFFGNPRKS KLICQATGFS PRQIQVSWLR EGKQVGSGVT TDQVQAEAKE SGPTTYKVTS TLTIKESDWL GQSMFTCRVD HRGLTFQQNA SSMCVPDQDT AIRVFAIPPS FASIFLTKST KLTCLVTDLT TYDSVTISWT RQNGEAVKTH TNISESHPNA TFSAVGEASI CEDDWNSGER FTCTVTHTDL PSPLKQTISR PKGVALHRPD VYLLPPAREQ LNLRESATIT CLVTGFSPAD VFVQWMQRGQ PLSPEKYVTS AMPEPQAPGR YFAHSILTVS EEEWNTGETY TCVVAHEALP NRVTERTVDK STGKPTLYNV SLVMSDTAGT CY

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Macromolecule #3: human IgM light chain

MacromoleculeName: human IgM light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASETVS NDKVAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSISGLE PEDFVVYYCQ QYASSPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK ...String:
EIVLTQSPGT LSLSPGERAT LSCRASETVS NDKVAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSISGLE PEDFVVYYCQ QYASSPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 34.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 128440 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 301286
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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