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- PDB-7yte: crystal structure of human FcmR-D1 bound to IgM C4-domain -

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Basic information

Entry
Database: PDB / ID: 7yte
Titlecrystal structure of human FcmR-D1 bound to IgM C4-domain
Components
  • Fas apoptotic inhibitory molecule 3
  • Ig mu chain C region secreted form
KeywordsIMMUNE SYSTEM / FcmR / immunoglobin M
Function / homology
Function and homology information


high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / Fc receptor-mediated immune complex endocytosis / humoral immune response mediated by circulating immunoglobulin / cellular defense response / trans-Golgi network membrane / transmembrane signaling receptor activity ...high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / Fc receptor-mediated immune complex endocytosis / humoral immune response mediated by circulating immunoglobulin / cellular defense response / trans-Golgi network membrane / transmembrane signaling receptor activity / early endosome membrane / lysosomal membrane / centrosome / negative regulation of apoptotic process / Golgi apparatus / signal transduction / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin mu Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, Y. / Shen, H. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nature / Year: 2023
Title: Immunoglobulin M perception by FcμR.
Authors: Yaxin Li / Hao Shen / Ruixue Zhang / Chenggong Ji / Yuxin Wang / Chen Su / Junyu Xiao /
Abstract: Immunoglobulin M (IgM) is the first antibody to emerge during embryonic development and the humoral immune response. IgM can exist in several distinct forms, including monomeric, membrane-bound IgM ...Immunoglobulin M (IgM) is the first antibody to emerge during embryonic development and the humoral immune response. IgM can exist in several distinct forms, including monomeric, membrane-bound IgM within the B cell receptor (BCR) complex, pentameric and hexameric IgM in serum and secretory IgM on the mucosal surface. FcμR, the only IgM-specific receptor in mammals, recognizes different forms of IgM to regulate diverse immune responses. However, the underlying molecular mechanisms remain unknown. Here we delineate the structural basis of the FcμR-IgM interaction by crystallography and cryo-electron microscopy. We show that two FcμR molecules interact with a Fcμ-Cμ4 dimer, suggesting that FcμR can bind to membrane-bound IgM with a 2:1 stoichiometry. Further analyses reveal that FcμR-binding sites are accessible in the context of IgM BCR. By contrast, pentameric IgM can recruit four FcμR molecules to bind on the same side and thereby facilitate the formation of an FcμR oligomer. One of these FcμR molecules occupies the binding site of the secretory component. Nevertheless, four FcμR molecules bind to the other side of secretory component-containing secretory IgM, consistent with the function of FcμR in the retrotransport of secretory IgM. These results reveal intricate mechanisms of IgM perception by FcμR.
History
DepositionAug 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / diffrn ...atom_site / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / refine / reflns / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_seq_id / _diffrn.ambient_temp ..._atom_site.label_seq_id / _diffrn.ambient_temp / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.ls_number_reflns_obs / _reflns.number_obs / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ncs_dom_lim.selection_details
Revision 2.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig mu chain C region secreted form
B: Ig mu chain C region secreted form
D: Fas apoptotic inhibitory molecule 3
C: Fas apoptotic inhibitory molecule 3


Theoretical massNumber of molelcules
Total (without water)48,3534
Polymers48,3534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-17 kcal/mol
Surface area21610 Å2
Unit cell
Length a, b, c (Å)85.718, 85.718, 60.676
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 446 through 557)
21chain B
12(chain C and resid 20 through 124)
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY(chain A and resid 446 through 557)AA446 - 5571 - 112
21GLYGLYGLYGLYchain BBB446 - 5571 - 112
12LEULEUSERSER(chain C and resid 20 through 124)CD20 - 1243 - 107
22ARGARGSERSERchain DDC18 - 1241 - 107

NCS ensembles :
ID
1
2

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Components

#1: Protein Ig mu chain C region secreted form


Mass: 12452.974 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein Fas apoptotic inhibitory molecule 3 / IgM Fc fragment receptor / Regulator of Fas-induced apoptosis Toso


Mass: 11723.567 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCMR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60667
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1:1 ratio of protein:reservoir solution containing 0.1 M Ammonium citrate tribasic (pH 7.0) and 12% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.00895 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00895 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9518 / % possible obs: 95.35 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.9
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.363 / Num. unique obs: 2435

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KXS

6kxs


Resolution: 3→28.08 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 491 5.16 %
Rwork0.2299 9028 -
obs0.232 9518 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.44 Å2 / Biso mean: 48.2095 Å2 / Biso min: 20.9 Å2
Refinement stepCycle: final / Resolution: 3→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 0 0 3363
Num. residues----436
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A680X-RAY DIFFRACTION11.961TORSIONAL
12B680X-RAY DIFFRACTION11.961TORSIONAL
21C634X-RAY DIFFRACTION11.961TORSIONAL
22D634X-RAY DIFFRACTION11.961TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.30.38871260.32112235236194
3.3-3.780.29151240.27732261238596
3.78-4.760.26431220.20692289241197
4.76-28.080.21371190.18842243236295

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