+Open data
-Basic information
Entry | Database: PDB / ID: 5lpu | ||||||
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Title | Crystal structure of Annexin A2 complexed with S100A4 | ||||||
Components |
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Keywords | calcium-binding protein / protein-protein complex | ||||||
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 / RAGE receptor binding / 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 / Dissolution of Fibrin Clot / S100 protein binding / virion binding / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / chemoattractant activity / positive regulation of exocytosis / transition metal ion binding / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / epithelial to mesenchymal transition / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate 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 / actin binding / midbody / basolateral plasma membrane / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ecsedi, P. / Gogl, G. / Kiss, B. / Nyitray, L. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Regulation of the Equilibrium between Closed and Open Conformations of Annexin A2 by N-Terminal Phosphorylation and S100A4-Binding. Authors: Ecsedi, P. / Kiss, B. / Gogl, G. / Radnai, L. / Buday, L. / Koprivanacz, K. / Liliom, K. / Leveles, I. / Vertessy, B. / Jeszenoi, N. / Hetenyi, C. / Schlosser, G. / Katona, G. / Nyitray, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lpu.cif.gz | 367.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lpu.ent.gz | 301.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lpu_validation.pdf.gz | 470.2 KB | Display | wwPDB validaton report |
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Full document | 5lpu_full_validation.pdf.gz | 476.6 KB | Display | |
Data in XML | 5lpu_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 5lpu_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/5lpu ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lpu | HTTPS FTP |
-Related structure data
Related structure data | 5lpxC 5lq0C 5lq2C 2hywS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38613.941 Da / Num. of mol.: 2 / Mutation: A66E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: P07355 #2: Protein | Mass: 12027.813 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S100A4, CAPL, MTS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P26447 #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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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: 3.21 Å3/Da / Density % sol: 61.71 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis Tris pH 6.5, 0.2M ammonium acetate 4% PEG4000 and 1,5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.374 Å / Num. obs: 75455 / % possible obs: 99.98 % / Redundancy: 13.6 % / Rsym value: 0.067 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.1→2.17 Å / Mean I/σ(I) obs: 2.42 / % possible all: 99.87 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HYW Resolution: 2.1→49.374 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.374 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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