+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13922 | |||||||||||||||||||||
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Title | Cryo-EM structure of human monomeric IgM-Fc | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Function / homology | Isoform 2 of Immunoglobulin heavy constant mu Function and homology information | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
Authors | Chen Q / Rosenthal P / Tolar P | |||||||||||||||||||||
Funding support | United Kingdom, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13922.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-13922-v30.xml emd-13922.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13922_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_13922.png | 55.9 KB | ||
Masks | emd_13922_msk_1.map | 64 MB | Mask map | |
Others | emd_13922_half_map_1.map.gz emd_13922_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13922 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13922 | HTTPS FTP |
-Validation report
Summary document | emd_13922_validation.pdf.gz | 554.3 KB | Display | EMDB validaton report |
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Full document | emd_13922_full_validation.pdf.gz | 553.8 KB | Display | |
Data in XML | emd_13922_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_13922_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13922 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13922 | HTTPS FTP |
-Related structure data
Related structure data | 7qdoMC 8adyC 8adzC 8ae0C 8ae2C 8ae3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13922.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.839 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13922_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13922_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13922_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human monomeric IgM-Fc
Entire | Name: human monomeric IgM-Fc |
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Components |
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-Supramolecule #1: human monomeric IgM-Fc
Supramolecule | Name: human monomeric IgM-Fc / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Isoform 2 of Immunoglobulin heavy constant mu
Macromolecule | Name: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.687059 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GVIAELPPKV SVFVPPRDGF FGNPRKSKLI CQATGFSPRQ IQVSWLREGK QVGSGVTTD QVQAEAKESG PTTYKVTSTL TIKESDWLSQ SMFTCRVDHR GLTFQQNASS MCVPDQDTAI RVFAIPPSFA S IFLTKSTK ...String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GVIAELPPKV SVFVPPRDGF FGNPRKSKLI CQATGFSPRQ IQVSWLREGK QVGSGVTTD QVQAEAKESG PTTYKVTSTL TIKESDWLSQ SMFTCRVDHR GLTFQQNASS MCVPDQDTAI RVFAIPPSFA S IFLTKSTK LTCLVTDLTT YDSVTISWTR QNGEAVKTHT NISESHPNAT FSAVGEASIS EDDWNSGERF TCTVTHTDLP SP LKQTISR PKGVALHRPD VYLLPPAREQ LNLRESATIT CLVTGFSPAD VFVQWMQRGQ PLSPEKYVTS APMPEPQAPG RYF AHSILT VSEEEWNTGE TYTCVVAHEA LPNRVTERTV DKSTEGEVSA DEEGFENEIA QLEYEISQLE QEIQALESGG GSGG GSENL YFQGGGSWSH PQFEKGGGSG GGSGGSAWSH PQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 59595 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-7qdo: |