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- PDB-9x35: high affinity IgG1 Fc variant in complex with Fc gamma receptor I... -

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Basic information

Entry
Database: PDB / ID: 9x35
Titlehigh affinity IgG1 Fc variant in complex with Fc gamma receptor IIIA 158F
Components
  • (IgG1 Fc variant chain ...) x 2
  • Fc gama recepror IIIa 158F
KeywordsIMMUNE SYSTEM / IgG1 Fc variant / Fc gamma receptor IIIA 158F receptor / complex
Biological speciesVector pcDNA3.1-GFP (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsLonglong, L. / Yangyihua, Z. / Jiannan, F. / Xiang, G. / Yaowei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82204262 China
CitationJournal: To Be Published
Title: high affinity IgG1 Fc variant in complex with Fc gamma receptor IIIA
Authors: Longlong, L. / Yangyihua, Z.
History
DepositionOct 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 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

Downloads & links

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Assembly

Deposited unit
A: Fc gama recepror IIIa 158F
B: IgG1 Fc variant chain B
C: IgG1 Fc variant chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1647
Polymers67,3313
Non-polymers2,8334
Water00
1


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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fc gama recepror IIIa 158F


Mass: 19460.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Number starts from 6 / Source: (gene. exp.) Vector pcDNA3.1-GFP (others) / Production host: Cricetulus griseus (Chinese hamster)

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Antibody , 2 types, 2 molecules BC

#2: Antibody IgG1 Fc variant chain B


Mass: 23813.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Number starts from 235 / Source: (gene. exp.) Vector pcDNA3.1-GFP (others) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody IgG1 Fc variant chain C


Mass: 24056.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Number starts from 233 / Source: (gene. exp.) Vector pcDNA3.1-GFP (others) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 3 types, 4 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Details

Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1Crystal structure of human IgG1-Fc variant in complex with Fc gamma receptor IIIa 158FCOMPLEX#1-#30RECOMBINANT
2IgG1-Fc variantCOMPLEX#2-#31RECOMBINANT
3Fc gama recepror IIIa 158FCOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Cricetulus griseus (Chinese hamster)10029
32Cricetulus griseus (Chinese hamster)10029
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 736617 / Symmetry type: POINT
RefinementHighest resolution: 2.81 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034988
ELECTRON MICROSCOPYf_angle_d0.5346795
ELECTRON MICROSCOPYf_dihedral_angle_d6.216743
ELECTRON MICROSCOPYf_chiral_restr0.043801
ELECTRON MICROSCOPYf_plane_restr0.004846

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