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- EMDB-49625: Structure of human annexin A1 in complex with 2C1 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-49625
TitleStructure of human annexin A1 in complex with 2C1 Fab
Map data
Sample
  • Complex: Antigen-Fab complex
    • Protein or peptide: Annexin A1
    • Protein or peptide: 2C1 Fab heavy chain
    • Protein or peptide: 2C1 Fab light chain
KeywordsAnnexin A1 / ANXA1 / Anti-Annexin A1 Antibody / Fab / PROTEIN BINDING / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of interleukin-1 production / myoblast migration involved in skeletal muscle regeneration / granulocyte chemotaxis / regulation of leukocyte migration / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / peptide cross-linking / regulation of hormone secretion / neutrophil clearance / cadherin binding involved in cell-cell adhesion ...regulation of interleukin-1 production / myoblast migration involved in skeletal muscle regeneration / granulocyte chemotaxis / regulation of leukocyte migration / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / peptide cross-linking / regulation of hormone secretion / neutrophil clearance / cadherin binding involved in cell-cell adhesion / positive regulation of vesicle fusion / cornified envelope / neutrophil activation / negative regulation of interleukin-8 production / positive regulation of neutrophil apoptotic process / neutrophil homeostasis / calcium-dependent phospholipid binding / negative regulation of T-helper 2 cell differentiation / Formyl peptide receptors bind formyl peptides and many other ligands / motile cilium / vesicle membrane / alpha-beta T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / arachidonate secretion / negative regulation of exocytosis / cellular response to glucocorticoid stimulus / positive regulation of wound healing / phosphatidylserine binding / monocyte chemotaxis / cellular response to vascular endothelial growth factor stimulus / lateral plasma membrane / Smooth Muscle Contraction / phagocytosis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of interleukin-2 production / keratinocyte differentiation / phagocytic cup / positive regulation of T cell proliferation / Developmental Lineage of Pancreatic Ductal Cells / adherens junction / phospholipid binding / sarcolemma / calcium-dependent protein binding / regulation of cell shape / extracellular matrix / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / early endosome membrane / G alpha (i) signalling events / vesicle / G alpha (q) signalling events / basolateral plasma membrane / adaptive immune response / cell surface receptor signaling pathway / endosome / apical plasma membrane / inflammatory response / signaling receptor binding / innate immune response / focal adhesion / calcium ion binding / lipid binding / negative regulation of apoptotic process / cell surface / signal transduction / : / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Annexin A1 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsNadezhdin KD / Sobolevsky AI
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR078814 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA206573 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS107253 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA192111 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE029532 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA013696 United States
CitationJournal: To Be Published
Title: Annexin A1 plays an essential dual role throughout neoplastic progression by stimulating tumor growth and modulating immune microenvironment via direct binding of beta-catenin
Authors: Nadezhdin KD / Sovolevsky AI
History
DepositionMar 10, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49625.png

Downloads & links

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Map

FileDownload / File: emd_49625.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 220 pix.
= 230.12 Å		1.05 Å/pix.
x 220 pix.
= 230.12 Å		1.05 Å/pix.
x 220 pix.
= 230.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00242
Minimum - Maximum-0.024637455 - 0.032988105
Average (Standard dev.)0.00001520049 (±0.0004916717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 230.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49625_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49625_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 : Antigen-Fab complex

EntireName: Antigen-Fab complex
Components
  • Complex: Antigen-Fab complex
    • Protein or peptide: Annexin A1
    • Protein or peptide: 2C1 Fab heavy chain
    • Protein or peptide: 2C1 Fab light chain

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Supramolecule #1: Antigen-Fab complex

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

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Macromolecule #1: Annexin A1

MacromoleculeName: Annexin A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.181688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMAMVS EFLKQAWFIE NEEQEYVQTV KSSKGGPGSA VSPYPTFNPS SDVAALHKAI MVKGVDEATI IDILTKRNNA QRQQIKAAY LQETGKPLDE TLKKALTGHL EEVVLALLKT PAQFDADELR AAMKGLGTDE DTLIEILASR TNKEIRDINR V YREELKRD ...String:
GPLGSMAMVS EFLKQAWFIE NEEQEYVQTV KSSKGGPGSA VSPYPTFNPS SDVAALHKAI MVKGVDEATI IDILTKRNNA QRQQIKAAY LQETGKPLDE TLKKALTGHL EEVVLALLKT PAQFDADELR AAMKGLGTDE DTLIEILASR TNKEIRDINR V YREELKRD LAKDITSDTS GDFRNALLSL AKGDRSEDFG VNEDLADSDA RALYEAGERR KGTDVNVFNT ILTTRSYPQL RR VFQKYTK YSKHDMNKVL DLELKGDIEK CLTAIVKCAT SKPAFFAEKL HQAMKGVGTR HKALIRIMVS RSEIDMNDIK AFY QKMYGI SLCQAILDET KGDYEKILVA LCGGN

UniProtKB: Annexin A1

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Macromolecule #2: 2C1 Fab heavy chain

MacromoleculeName: 2C1 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.106027 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVKLVESGGG LVQPGGSLRL SCAISGFTFS DFYMEWVRQF PGKRLEWVAA SKNKANDYTT EYSASVKGRF IVSRDTSQSI LYLQMNALR AEDTAIYYCA AGGYDEGVGW YFDVWGAGTT VTVSSAAKTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP E PVTVTWNS ...String:
EVKLVESGGG LVQPGGSLRL SCAISGFTFS DFYMEWVRQF PGKRLEWVAA SKNKANDYTT EYSASVKGRF IVSRDTSQSI LYLQMNALR AEDTAIYYCA AGGYDEGVGW YFDVWGAGTT VTVSSAAKTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP E PVTVTWNS GSLSSGVHTF PAVLQSDLYT LSSSVTVPSS TWPSETVTCN VAHPASSTKV DKKIVPR

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Macromolecule #3: 2C1 Fab light chain

MacromoleculeName: 2C1 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.564914 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVMTQSQKF MSTSVGDRVS VTCKASQNVG TNVAWFQQKP GLSPKPLIYS ASYRYRGVPD RFTGSASGTD FTLTISSVQS EDLAEYFCQ QYNNYPYTFG GGTRLEINRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVMTQSQKF MSTSVGDRVS VTCKASQNVG TNVAWFQQKP GLSPKPLIYS ASYRYRGVPD RFTGSASGTD FTLTISSVQS EDLAEYFCQ QYNNYPYTFG GGTRLEINRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRN

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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: 7.4 / Component - Concentration: 1.0 x / Component - Name: PBS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8312 / Average exposure time: 0.8 sec. / 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: 1.8 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 103796
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9np0:
Structure of human annexin A1 in complex with 2C1 Fab

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