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- EMDB-15377: Cryo-EM structure of full-length human immunoglobulin M - F(ab')2... -

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Basic information

Entry
Database: EMDB / ID: EMD-15377
TitleCryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 3
Map data
Sample
  • Complex: Full-length human IgM pentamer
    • Protein or peptide: IgM Fab, light chain
    • Protein or peptide: IgM Fab, heavy chain
    • Protein or peptide: IgM C2-domain from mouse
    • Protein or peptide: Immunoglobulin heavy constant mu
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsfull-length human immunoglobulin M / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 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
DepositionJul 12, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15377.png

Downloads & links

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Map

FileDownload / File: emd_15377.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 300 pix.
= 654. Å		2.18 Å/pix.
x 300 pix.
= 654. Å		2.18 Å/pix.
x 300 pix.
= 654. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-1.2921236 - 6.6567645
Average (Standard dev.)-0.0000054371494 (±0.1735894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 654.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15377_msk_1.map
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Additional map: #1

Fileemd_15377_additional_1.map
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Half map: #2

Fileemd_15377_half_map_1.map
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Half map: #1

Fileemd_15377_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: IgM Fab, light chain
    • Protein or peptide: IgM Fab, heavy chain
    • Protein or peptide: IgM C2-domain from mouse
    • Protein or peptide: Immunoglobulin heavy constant mu
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: IgM Fab, light chain

MacromoleculeName: IgM Fab, light chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.367873 KDa
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASETVS NDKVAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSISGLE PEDFVVYYC QQYASSPRTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPGT LSLSPGERAT LSCRASETVS NDKVAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSISGLE PEDFVVYYC QQYASSPRTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #2: IgM Fab, heavy chain

MacromoleculeName: IgM Fab, heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.57473 KDa
SequenceString: QVTLKESGPT LVKPTQTLTL TCTFSGFSLT TTGEGVGWIR QPPGKALEFL AFIYWNDAKR YNPSLQSRLT ITKDASKKQV VLTLTNLDP VDTATYYCAR TSGWDIEFEY WGQGTLVTVS SGSASAPTLF PLVSCENSSP SSTVAVGCLA QDFLPDSITF S WKYKNNSD ...String:
QVTLKESGPT LVKPTQTLTL TCTFSGFSLT TTGEGVGWIR QPPGKALEFL AFIYWNDAKR YNPSLQSRLT ITKDASKKQV VLTLTNLDP VDTATYYCAR TSGWDIEFEY WGQGTLVTVS SGSASAPTLF PLVSCENSSP SSTVAVGCLA QDFLPDSITF S WKYKNNSD ISSTRGFPSV LRGGKYAATS QVLLPSKDVM QGTDEHVVCK VQHPNGNKEK DVPLPVVI

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Macromolecule #3: IgM C2-domain from mouse

MacromoleculeName: IgM C2-domain from mouse / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.769625 KDa
SequenceString:
MGIPAVAEMN PNVNVFVPPR DGFSGPAPRK SKLICEATNF TPKPITVSWL KDGKLVESGF TTDPVTIENK GSTPQTYKVI STLTISEID WLNLNVYTCR VDHRGLTFLK NVSSTCAA

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Macromolecule #4: Immunoglobulin heavy constant mu

MacromoleculeName: Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.875766 KDa
SequenceString: ASAWSHPQFE KGGGSGGGSG GSAWSHPQFE KIDTTIAELP PKVSVFVPPR DGFFGNPRKS KLICQATGFS PRQIQVSWLR EGKQVGSGV TTDQVQAEAK ESGPTTYKVT STLTIKESDW LGQSMFTCRV DHRGLTFQQN ASSMCVPDQD TAIRVFAIPP S FASIFLTK ...String:
ASAWSHPQFE KGGGSGGGSG GSAWSHPQFE KIDTTIAELP PKVSVFVPPR DGFFGNPRKS KLICQATGFS PRQIQVSWLR EGKQVGSGV TTDQVQAEAK ESGPTTYKVT STLTIKESDW LGQSMFTCRV DHRGLTFQQN ASSMCVPDQD TAIRVFAIPP S FASIFLTK STKLTCLVTD LTTYDSVTIS WTRQNGEAVK THTNISESHP NATFSAVGEA SICEDDWNSG ERFTCTVTHT DL PSPLKQT ISRPKGVALH RPDVYLLPPA REQLNLRESA TITCLVTGFS PADVFVQWMQ RGQPLSPEKY VTSAPMPEPQ APG RYFAHS ILTVSEEEWN TGETYTCVVA HEALPNRVTE RTVDKSTGKP TLYNVSLVMS DTAGTCY

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Macromolecule #5: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.483329 KDa
SequenceString:
EDERIVLVDN KCKCARITSR IIRSSEDPNE DIVERNIRII VPLNNRENIS DPTSPLRTRF VYHLSDLCKK CDPTEVELDN QIVTATQSN ICDEDSATET CYTYDRNKCY TAVVPLVYGG ETKMVETALT PDACYPD

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 10 / 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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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 magnification: 128440 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / 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

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

6kxs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26368
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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