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

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Basic information

Entry
Database: PDB / ID: 9np0
TitleStructure of human annexin A1 in complex with 2C1 Fab
Components
  • 2C1 Fab heavy chain
  • 2C1 Fab light chain
  • Annexin A1
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / Annexin 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsNadezhdin, K.D. / Sobolevsky, A.I.
Funding support United States, 7items
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, K.D. / Sovolevsky, A.I.
History
DepositionMar 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / 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: Annexin A1
B: 2C1 Fab heavy chain
C: 2C1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)86,8533
Polymers86,8533
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Annexin A1 / Annexin I / Annexin-1 / Calpactin II / Calpactin-2 / Chromobindin-9 / Lipocortin I / Phospholipase ...Annexin I / Annexin-1 / Calpactin II / Calpactin-2 / Chromobindin-9 / Lipocortin I / Phospholipase A2 inhibitory protein / p35


Mass: 39181.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA1, ANX1, LPC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04083
#2: Antibody 2C1 Fab heavy chain


Mass: 24106.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody 2C1 Fab light chain


Mass: 23564.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
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

ComponentName: Antigen-Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Buffer componentConc.: 1 x / Name: PBS
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: 1800 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 0.8 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8312

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
12RELION53D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103796 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058388
ELECTRON MICROSCOPYf_angle_d1.07615119
ELECTRON MICROSCOPYf_dihedral_angle_d13.0333361
ELECTRON MICROSCOPYf_chiral_restr0.058641
ELECTRON MICROSCOPYf_plane_restr0.0061295

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