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- PDB-6kxs: Cryo-EM structure of human IgM-Fc in complex with the J chain and... -

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Basic information

Entry
Database: PDB / ID: 6kxs
TitleCryo-EM structure of human IgM-Fc in complex with the J chain and the ectodomain of pIgR
Components
  • Immunoglobulin J chain
  • Immunoglobulin heavy constant mu
  • Polymeric immunoglobulin receptor
KeywordsIMMUNE SYSTEM / immunoglobulin / pentamer / transcytosis / secreted
Function / homology
Function and homology information


polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / hexameric IgM immunoglobulin complex / polymeric immunoglobulin binding / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / secretory IgA immunoglobulin complex ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / hexameric IgM immunoglobulin complex / polymeric immunoglobulin binding / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / IgA binding / pre-B cell allelic exclusion / IgM immunoglobulin complex / glomerular filtration / detection of chemical stimulus involved in sensory perception of bitter taste / CD22 mediated BCR regulation / immunoglobulin receptor binding / azurophil granule membrane / receptor clustering / positive regulation of respiratory burst / humoral immune response / Scavenging of heme from plasma / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / transmembrane signaling receptor activity / antibacterial humoral response / protein-containing complex assembly / protein-macromolecule adaptor activity / blood microparticle / defense response to Gram-negative bacterium / Potential therapeutics for SARS / adaptive immune response / receptor complex / immune response / innate immune response / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin J chain / Immunoglobulin J chain / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype ...Immunoglobulin J chain / Immunoglobulin J chain / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin J chain / Polymeric immunoglobulin receptor / Immunoglobulin heavy constant mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, Y. / Wang, G. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Science / Year: 2020
Title: Structural insights into immunoglobulin M.
Authors: Yaxin Li / Guopeng Wang / Ningning Li / Yuxin Wang / Qinyu Zhu / Huarui Chu / Wenjun Wu / Ying Tan / Feng Yu / Xiao-Dong Su / Ning Gao / Junyu Xiao /
Abstract: Immunoglobulin M (IgM) plays a pivotal role in both humoral and mucosal immunity. Its assembly and transport depend on the joining chain (J-chain) and the polymeric immunoglobulin receptor (pIgR), ...Immunoglobulin M (IgM) plays a pivotal role in both humoral and mucosal immunity. Its assembly and transport depend on the joining chain (J-chain) and the polymeric immunoglobulin receptor (pIgR), but the underlying molecular mechanisms of these processes are unclear. We report a cryo-electron microscopy structure of the Fc region of human IgM in complex with the J-chain and pIgR ectodomain. The IgM-Fc pentamer is formed asymmetrically, resembling a hexagon with a missing triangle. The tailpieces of IgM-Fc pack into an amyloid-like structure to stabilize the pentamer. The J-chain caps the tailpiece assembly and bridges the interaction between IgM-Fc and the polymeric immunoglobulin receptor, which undergoes a large conformational change to engage the IgM-J complex. These results provide a structural basis for the function of IgM.
History
DepositionSep 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
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Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
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Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
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Structure visualization

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Assembly

Deposited unit
A: Immunoglobulin heavy constant mu
B: Immunoglobulin heavy constant mu
C: Immunoglobulin heavy constant mu
D: Immunoglobulin heavy constant mu
E: Immunoglobulin heavy constant mu
F: Immunoglobulin heavy constant mu
G: Immunoglobulin heavy constant mu
H: Immunoglobulin heavy constant mu
K: Immunoglobulin heavy constant mu
L: Immunoglobulin heavy constant mu
J: Immunoglobulin J chain
P: Polymeric immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,24923
Polymers495,61312
Non-polymers2,63611
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
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: 41875.766 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: N-ACETYL-D-GLUCOSAMINE / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01871
#2: Protein Immunoglobulin J chain / Joining chain of multimeric IgA and IgM


Mass: 15483.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JCHAIN, IGCJ, IGJ / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01591
#3: Protein Polymeric immunoglobulin receptor / Poly-Ig receptor / Hepatocellular carcinoma-associated protein TB6


Mass: 61371.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIGR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01833
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
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: Ternary complex of IgM-Fc with the J chain and pIgR/SC
Type: COMPLEX / Entity ID: #3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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
Image recordingElectron dose: 59.74 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1183008 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01823046
ELECTRON MICROSCOPYf_angle_d1.39131493
ELECTRON MICROSCOPYf_dihedral_angle_d6.07813846
ELECTRON MICROSCOPYf_chiral_restr0.0883690
ELECTRON MICROSCOPYf_plane_restr0.0114037

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