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- EMDB-76947: Cryo-EM structure of AZGP1-Fab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-76947
TitleCryo-EM structure of AZGP1-Fab complex
Map datastructure of AZGP1-Fab complex
Sample
  • Complex: AZGP1-Fab complex
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
    • Protein or peptide: Zinc-alpha-2-glycoprotein
KeywordsAdipokine / Secreted glycoprotein / Antigen antibody interaction / Zinc alpha2 glycoprotein / LIPID BINDING PROTEIN / LIPID BINDING PROTEIN-Immune System complex
Function / homology
Function and homology information


Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / transmembrane protein transporter activity / RNA nuclease activity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of T cell mediated cytotoxicity / cell adhesion / immune response / negative regulation of cell population proliferation ...Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / transmembrane protein transporter activity / RNA nuclease activity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of T cell mediated cytotoxicity / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / : / extracellular exosome / extracellular region / nucleus
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Zinc-alpha-2-glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMedina E / Joseph JS / Gowda M / Shanehsazzadeh A / Panwar P
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: CryoEM structure of AZGP1-Fab complex
Authors: Levine S / Shanehsazzadeh A
History
DepositionApr 28, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76947.png

Downloads & links

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Map

FileDownload / File: emd_76947.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of AZGP1-Fab complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.11001479 - 0.14772192
Average (Standard dev.)-0.000006151161 (±0.0037407437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_76947_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_76947_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AZGP1-Fab complex

EntireName: AZGP1-Fab complex
Components
  • Complex: AZGP1-Fab complex
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
    • Protein or peptide: Zinc-alpha-2-glycoprotein

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Supramolecule #1: AZGP1-Fab complex

SupramoleculeName: AZGP1-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.507236 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIVMTQSPLS LPVTPGEPAS ISCRSSQSIP YNLLDWYLQK SGQSPQLLIY LASNRASGVP DRFSGSGSGT DFTLKISRVE AEDVGFYYC MQGLETPLTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSIP YNLLDWYLQK SGQSPQLLIY LASNRASGVP DRFSGSGSGT DFTLKISRVE AEDVGFYYC MQGLETPLTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #2: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.541293 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LEQPGGSLRL SCAGSGFTFS SYGMTWVRQA PGKGLEWVSS ISSSGYYTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD LGTLLGSLGM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
EVQLVESGGG LEQPGGSLRL SCAGSGFTFS SYGMTWVRQA PGKGLEWVSS ISSSGYYTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD LGTLLGSLGM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HTGSGSDYKD DD DK

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Macromolecule #3: Zinc-alpha-2-glycoprotein

MacromoleculeName: Zinc-alpha-2-glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.012746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QENQDGRYSL TYIYTGLSKH VEDVPAFQAL GSLNDLQFFR YNSKDRKSQP MGLWRQVEGM EDWKQDSQLQ KAREDIFMET LKDIVEYYN DSNGSHVLQG RFGCEIENNR SSGAFWKYYY DGKDYIEFNK EIPAWVPFDP AAQITKQKWE AEPVYVQRAK A YLEEECPA ...String:
QENQDGRYSL TYIYTGLSKH VEDVPAFQAL GSLNDLQFFR YNSKDRKSQP MGLWRQVEGM EDWKQDSQLQ KAREDIFMET LKDIVEYYN DSNGSHVLQG RFGCEIENNR SSGAFWKYYY DGKDYIEFNK EIPAWVPFDP AAQITKQKWE AEPVYVQRAK A YLEEECPA TLRKYLKYSK NILDRQDPPS VVVTSHQAPG EKKKLKCLAY DFYPGKIDVH WTRAGEVQEP ELRGDVLHNG NG TYQSWVV VAVPPQDTAP YSCHVQHSSL AQPLVVPWEA SHHHHHH

UniProtKB: Zinc-alpha-2-glycoprotein

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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: TFS FALCON 4i (4k x 4k) / Average electron dose: 1.225 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 435000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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