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- EMDB-66494: high affinity IgG1 Fc variant in complex with Fc gamma receptor I... -

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Basic information

Entry
Database: EMDB / ID: EMD-66494
Titlehigh affinity IgG1 Fc variant in complex with Fc gamma receptor IIIA 158F
Map data
Sample
  • Complex: Crystal structure of human IgG1-Fc variant in complex with Fc gamma receptor IIIa 158F
    • Complex: IgG1-Fc variant
      • Protein or peptide: IgG1 Fc variant chain B
      • Protein or peptide: IgG1 Fc variant chain C
    • Complex: Fc gama recepror IIIa 158F
      • Protein or peptide: Fc gama recepror IIIa 158F
KeywordsIgG1 Fc variant / Fc gamma receptor IIIA 158F receptor / complex / IMMUNE SYSTEM
Biological speciesHomo sapiens (human) / Vector pcDNA3.1-GFP (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsLonglong L / Yangyihua Z / Jiannan F / Xiang G / Yaowei M
Funding support China, 1 items
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, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66494.png

Downloads & links

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Map

FileDownload / File: emd_66494.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.06771124 - 1.7172413
Average (Standard dev.)0.0010388365 (±0.025868291)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 206.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66494_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66494_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Crystal structure of human IgG1-Fc variant in complex with Fc gam...

EntireName: Crystal structure of human IgG1-Fc variant in complex with Fc gamma receptor IIIa 158F
Components
  • Complex: Crystal structure of human IgG1-Fc variant in complex with Fc gamma receptor IIIa 158F
    • Complex: IgG1-Fc variant
      • Protein or peptide: IgG1 Fc variant chain B
      • Protein or peptide: IgG1 Fc variant chain C
    • Complex: Fc gama recepror IIIa 158F
      • Protein or peptide: Fc gama recepror IIIa 158F

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Supramolecule #1: Crystal structure of human IgG1-Fc variant in complex with Fc gam...

SupramoleculeName: Crystal structure of human IgG1-Fc variant in complex with Fc gamma receptor IIIa 158F
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: IgG1-Fc variant

SupramoleculeName: IgG1-Fc variant / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Fc gama recepror IIIa 158F

SupramoleculeName: Fc gama recepror IIIa 158F / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

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Macromolecule #1: Fc gama recepror IIIa 158F

MacromoleculeName: Fc gama recepror IIIa 158F / type: protein_or_peptide / ID: 1 / Details: Number starts from 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vector pcDNA3.1-GFP (others)
Molecular weightTheoretical: 19.460736 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
PKAVVFLEPQ WYRVLEKDSV TLKCQGAYSP EDNSTQWFHN ESLISSQASS YFIDAATVDD SGEYRCQTNL STLSDPVQLE VHIGWLLLQ APRWVFKEED PIHLRCHSWK NTALHKVTYL QNGKGRKYFH HNSDFYIPKA TLKDSGSYFC RGLFGSKNVS S ETVNITIT QG

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Macromolecule #2: IgG1 Fc variant chain B

MacromoleculeName: IgG1 Fc variant chain B / type: protein_or_peptide / ID: 2 / Details: Number starts from 235 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vector pcDNA3.1-GFP (others)
Molecular weightTheoretical: 23.813953 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: LGGPDVFLLP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPAEE QYNATLRVVS VLTVLHQDWL NGKEYKCKV SNKALPAPIA ATISKAKGQP REPQVYTLPP SRDELTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT T PPVLDSDG ...String:
LGGPDVFLLP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPAEE QYNATLRVVS VLTVLHQDWL NGKEYKCKV SNKALPAPIA ATISKAKGQP REPQVYTLPP SRDELTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT T PPVLDSDG SFFLYSKLTV DKSRWQQGNV FSCSVMHEAL HNHYTQKSLS LSPGK

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Macromolecule #3: IgG1 Fc variant chain C

MacromoleculeName: IgG1 Fc variant chain C / type: protein_or_peptide / ID: 3 / Details: Number starts from 233 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vector pcDNA3.1-GFP (others)
Molecular weightTheoretical: 24.056225 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: ELLGGPDVFL LPPKPKDTLM ISRTPEVTCV VVDVSHEDPE VKFNWYVDGV EVHNAKTKPA EEQYNATLRV VSVLTVLHQD WLNGKEYKC KVSNKALPAP IAATISKAKG QPREPQVYTL PPSRDELTKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY K TTPPVLDS ...String:
ELLGGPDVFL LPPKPKDTLM ISRTPEVTCV VVDVSHEDPE VKFNWYVDGV EVHNAKTKPA EEQYNATLRV VSVLTVLHQD WLNGKEYKC KVSNKALPAP IAATISKAKG QPREPQVYTL PPSRDELTKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY K TTPPVLDS DGSFFLYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPGK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 736617
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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