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Yorodumi- PDB-7zvn: Crystal structure of human Annexin A2 in complex with full phosph... -
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-Basic information
Entry | Database: PDB / ID: 7zvn | ||||||
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Title | Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 1.87 A resolution | ||||||
Components |
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Keywords | LIPID BINDING PROTEIN / nucleic acid binding / ASO / antisense oligonucleotide / phosphorothioate | ||||||
Function / homology | Function and homology information positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair ...positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / collagen fibril organization / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Hyjek-Skladanowska, M. / Anderson, B. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Skowronek, K. / Seth, P. / Nowotny, M. | ||||||
Funding support | 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding. Authors: Hyjek-Skladanowska, M. / Anderson, B.A. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Poznanski, J.T. / Skowronek, K. / Seth, P. / Nowotny, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zvn.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zvn.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 7zvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/7zvn ftp://data.pdbj.org/pub/pdb/validation_reports/zv/7zvn | HTTPS FTP |
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-Related structure data
Related structure data | 7zvxC 5lpuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 3 molecules ACD
#1: Protein | Mass: 35150.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: first residue derived from the expression construct Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Plasmid: pET28_HisSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07355 |
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#2: DNA chain | Mass: 5294.467 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: (K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS)(PST)(PST)(AS)(PST)(GS) Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 368 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.86 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 4% w/v PEG 4000, 14% v/v glycerol, 0.03 M MgCl2/CaCl2, 0.1 M bicine/Trizma base pH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→43.75 Å / Num. obs: 36723 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.29 Å2 / CC1/2: 1 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.87→1.99 Å / Num. unique obs: 35540 / CC1/2: 0.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LPU Resolution: 1.87→43.75 Å / SU ML: 0.2346 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9019 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→43.75 Å
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Refine LS restraints |
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LS refinement shell |
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