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- EMDB-66376: Cryo-EM structure of the IgY-FcRY complex -

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Basic information

Entry
Database: EMDB / ID: EMD-66376
TitleCryo-EM structure of the IgY-FcRY complex
Map data
Sample
  • Complex: Cryo-EM structure of the IgY-FcRY complex
    • Protein or peptide: Ig-like domain-containing protein
    • Protein or peptide: yolk sac IgY receptor precursor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
  • Ligand: alpha-D-mannopyranose
KeywordsImmunoglobulin Y / IMMUNE SYSTEM
Function / homology
Function and homology information


: / 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 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
Similarity search - Domain/homology
Ig-like domain-containing protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsDeng M / Du S / Xiao J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the IgY-FcRY complex
Authors: Deng M / Du S / Xiao J
History
DepositionSep 27, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66376.png

Downloads & links

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Map

FileDownload / File: emd_66376.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6816857 - 1.0782634
Average (Standard dev.)-0.00032424144 (±0.027840102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66376_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_66376_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 : Cryo-EM structure of the IgY-FcRY complex

EntireName: Cryo-EM structure of the IgY-FcRY complex
Components
  • Complex: Cryo-EM structure of the IgY-FcRY complex
    • Protein or peptide: Ig-like domain-containing protein
    • Protein or peptide: yolk sac IgY receptor precursor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Cryo-EM structure of the IgY-FcRY complex

SupramoleculeName: Cryo-EM structure of the IgY-FcRY complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Ig-like domain-containing protein

MacromoleculeName: Ig-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 35.320715 KDa
SequenceString: EVQVLHASSC TPSQSESVEL LCLVTGFSPA SAEVEWLVDG VGGLLVASQS PAVRSGSTYS LSSRVNVSGT DWREGKSYSC RVRHPATNT VVEDHVKGCP DGAQSCSPIQ LYAIPPSPGE LYISLDAKLR CLVVNLPSDS SLSVTWTREK SGNLRPDPMV L QEHFNGTY ...String:
EVQVLHASSC TPSQSESVEL LCLVTGFSPA SAEVEWLVDG VGGLLVASQS PAVRSGSTYS LSSRVNVSGT DWREGKSYSC RVRHPATNT VVEDHVKGCP DGAQSCSPIQ LYAIPPSPGE LYISLDAKLR CLVVNLPSDS SLSVTWTREK SGNLRPDPMV L QEHFNGTY SASSAVPVST QDWLSGERFT CTVQHEELPL PLSKSVYRNT GPTTPPLIYP FAPHPEELSL SRVTLSCLVR GF RPRDIEI RWLRDHRAVP ATEFVTTAVL PEERTANGAG GDGDTFFVYS KMSVETAKWN GGTVFACMAV HEALPMRFSQ RTL QKQA

UniProtKB: Ig-like domain-containing protein

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Macromolecule #2: yolk sac IgY receptor precursor

MacromoleculeName: yolk sac IgY receptor precursor / type: protein_or_peptide / ID: 2
Details: Sequence reference for Gallus gallus (TAX ID 9031) is not available in UniProt at the time of biocuration. Genebank accession number is AAS02156.1
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 168.748078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGVLLLACC LLLGGRSLPR GDAALSRDEL PSLRNKGIFI IQSSGSNLCI KADTAGLVLE DCSQISKHML WKWVSNRRLF NIGRSSCLG LNISRPEQPL TMLECDSNRY SLWWNCDGRA LVGVSEYRLA VENSKRIVAK KKSDYQWIQY MSYDEDLCEH P FQETYTLL ...String:
MLGVLLLACC LLLGGRSLPR GDAALSRDEL PSLRNKGIFI IQSSGSNLCI KADTAGLVLE DCSQISKHML WKWVSNRRLF NIGRSSCLG LNISRPEQPL TMLECDSNRY SLWWNCDGRA LVGVSEYRLA VENSKRIVAK KKSDYQWIQY MSYDEDLCEH P FQETYTLL GNSFGFPCVF PFKYNNKWYY ECTRDGKEFE WCATTSYYEQ DEKWGFCPGV EHGCGTFWKE NPATHVCYQF NP SAVLSWH EARAACQAQG GDLLSITSPE EQSYLSNLSR QLNTTDAVLW TGLNRLEEGA GWQWSDGAPL VFVNWKADVS EDH SSENHC AVMSSKLKYG WKSYLCESGL PFVCKKYLNK IEQETLDTWK YYATRCDAGW YPYNRYCYRL HKEAKSWNDA LISC QSDSS GLISISSMAD AELLHNLLQR ENITETWIGL YNSNISVVFE WSDGTPVKFS YWHSQEPNTF QRAGQLCVSA QGPEG HWKV KKCEDKNFYI CKKAGEFNSV SSDAESSCPE GWERHGGYCY KIDSTPRSFE HASSGYFCPS ALVSVTNRFE QAFITS MIR SVVKSERTYF WIGLQDLNNT GEYVWLTKDG KNHSVSYTNW NKHQPRHSGG CVAMRGQDPV GYWEVKSCKN FKAMSLC KQ KISSYEEPEL TFQRHLSSCY FGWESEGNLL NCYKIFHREK ILMKRTWSEA ETLCQDFGAH LASFSHVYEE TFLNNLLY T IFDRTEERQF WIGFNRRNPF SGGTWQWSDR TPVVASFLES KYVEDDSRNC GVFKVNRTIF PAHCNEKREW ICKIPKGVK PKNPDWYIAE LPWSYYQGAE YLFHVNPTDW DTYEFICVWL RSEMATIHSA DEQAFIENKI KKLSDSDVHW WIGLHAESIS NEFRWKDGS QITYQNWNEG RDRYLRKPGK RCGFISSQTG RWDDENCTVS LPCICKRKSA WKIEKEIPKD QNPQGTCPKG W LHFGYKCF LIQIPKDPEH LRSWYSAQTF CSRYDGSLAS LEDELEQAFI TMNLFGRKTS VWIAFQGDDY EKWMNENPPR YS NWSPIEA VHRPRYNGVY VEEQVPLCTL VSNNPNFYFT GKWYLENCEK NYGFVCQKGQ DTSRHIVNAS EMYPVPDTLQ YAN RTYTLI RGNFTWSAAL KACMANGAEL VSIADQYHQS FLTIIVNRLG YNHWIGLFTA DNGLNFEWSD GTRSLFTFWE DDES QALGS CVYMDTSGRW KSTSCERLLP GAVCHVPPKK KLTEYKGLCS ESNVPWIKFK NSCYSFNTVL QGTSFDTAYE VCRNQ GSNL LTIKDEDENA FILEELHSFG YSVKMVWLNI LQVTDNETVS WFDGSPLNYS NWGIREPEFD HLKGNFCISL RTADGV WQI SPCREIKGFV CKKDADLDAA EPSKKQSYPG LAALAVFVTL VMLAAISFFL WCLYKQNNRF FHRILWVRNA YFPQINS DA PALEESILIS DFERDDN

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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Macromolecule #6: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 10 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration1.1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 127853
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE

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