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- PDB-21nx: Cryo-EM structure of mouse IgG2b-Fc in complex with FcgammaRIV -

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Basic information

Entry
Database: PDB / ID: 21nx
TitleCryo-EM structure of mouse IgG2b-Fc in complex with FcgammaRIV
Components
  • Isoform 2 of Immunoglobulin heavy constant gamma 2B
  • Low affinity immunoglobulin gamma Fc region receptor III-A
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


IgE receptor activity / Post-translational modification: synthesis of GPI-anchored proteins / dendritic cell antigen processing and presentation / low-affinity IgG receptor activity / GPI anchor binding / natural killer cell degranulation / Classical antibody-mediated complement activation / IgG receptor activity / FCGR activation / Role of phospholipids in phagocytosis ...IgE receptor activity / Post-translational modification: synthesis of GPI-anchored proteins / dendritic cell antigen processing and presentation / low-affinity IgG receptor activity / GPI anchor binding / natural killer cell degranulation / Classical antibody-mediated complement activation / IgG receptor activity / FCGR activation / Role of phospholipids in phagocytosis / immune receptor activity / Fc receptor-mediated immune complex endocytosis / Regulation of Complement cascade / positive regulation of type IIa hypersensitivity / Fc-gamma receptor III complex / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / Regulation of actin dynamics for phagocytic cup formation / neutrophil activation / IgE binding / positive regulation of type I hypersensitivity / IgG immunoglobulin complex / positive regulation of bone resorption / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG binding / phagocytosis, engulfment / immunoglobulin receptor binding / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / Neutrophil degranulation / positive regulation of phagocytosis / positive regulation of immune response / cellular response to lipopolysaccharide / antibacterial humoral response / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / : / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor III-A / Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsXu, S.R. / Du, S. / Xiao, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse IgG2b-Fc in complex with FcgammaRIV
Authors: Xu, S.R. / Du, S. / Xiao, J.Y.
History
DepositionDec 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low affinity immunoglobulin gamma Fc region receptor III-A
B: Isoform 2 of Immunoglobulin heavy constant gamma 2B
C: Isoform 2 of Immunoglobulin heavy constant gamma 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3956
Polymers84,7083
Non-polymers1,6873
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Low affinity immunoglobulin gamma Fc region receptor III-A / IgG Fc receptor III-A / CD16-2 / FcgammaRIV


Mass: 25763.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fcgr4, Fcgr3a / Production host: Homo sapiens (human) / References: UniProt: A0A0B4J1G0
#2: Protein Isoform 2 of Immunoglobulin heavy constant gamma 2B / Ig gamma-2B chain C region


Mass: 29472.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighg2b, Igh-3 / Production host: Homo sapiens (human) / References: UniProt: P01867
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 1 / Source method: obtained synthetically / 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: mouse Fc gamma 2b in complex with FcgammaRIV / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 680209 / Symmetry type: POINT
RefinementHighest resolution: 2.99 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0074975
ELECTRON MICROSCOPYf_angle_d0.7056763
ELECTRON MICROSCOPYf_dihedral_angle_d4.856694
ELECTRON MICROSCOPYf_chiral_restr0.045778
ELECTRON MICROSCOPYf_plane_restr0.005855

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