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- PDB-7qdo: Cryo-EM structure of human monomeric IgM-Fc -

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Basic information

Entry
Database: PDB / ID: 7qdo
TitleCryo-EM structure of human monomeric IgM-Fc
ComponentsIsoform 2 of Immunoglobulin heavy constant mu
KeywordsIMMUNE SYSTEM / human monomeric IgM-Fc
Function / homologyIsoform 2 of Immunoglobulin heavy constant mu
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen, Q. / Rosenthal, P. / Tolar, P.
Funding support United Kingdom, 6items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
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Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Isoform 2 of Immunoglobulin heavy constant mu
A: Isoform 2 of Immunoglobulin heavy constant mu


Theoretical massNumber of molelcules
Total (without water)95,3742
Polymers95,3742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1690 Å2
ΔGint-16 kcal/mol
Surface area23700 Å2

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Components

#1: Protein Isoform 2 of Immunoglobulin heavy constant mu / Ig mu chain C region / Ig mu chain C region BOT / Ig mu chain C region GAL / Ig mu chain C region OU


Mass: 47687.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Variant: VAR_003903 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P01871-2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human monomeric IgM-Fc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Calibrated magnification: 59595 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 961072 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033348
ELECTRON MICROSCOPYf_angle_d0.714586
ELECTRON MICROSCOPYf_dihedral_angle_d4.208446
ELECTRON MICROSCOPYf_chiral_restr0.045538
ELECTRON MICROSCOPYf_plane_restr0.005590

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