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Yorodumi- PDB-5ksj: Crystal structure of deoxygenated hemoglobin in complex with Sphi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ksj | |||||||||
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Title | Crystal structure of deoxygenated hemoglobin in complex with Sphingosine phosphate | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / Sphingosine-1-phosphate / Complex / ALLOSTERIC EFFECTOR | |||||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Ahmed, M.H. / Safo, M.K. / Xia, Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2017 Title: Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease. Authors: Sun, K. / D'Alessandro, A. / Ahmed, M.H. / Zhang, Y. / Song, A. / Ko, T.P. / Nemkov, T. / Reisz, J.A. / Wu, H. / Adebiyi, M. / Peng, Z. / Gong, J. / Liu, H. / Huang, A. / Wen, Y.E. / Wen, A. ...Authors: Sun, K. / D'Alessandro, A. / Ahmed, M.H. / Zhang, Y. / Song, A. / Ko, T.P. / Nemkov, T. / Reisz, J.A. / Wu, H. / Adebiyi, M. / Peng, Z. / Gong, J. / Liu, H. / Huang, A. / Wen, Y.E. / Wen, A.Q. / Berka, V. / Bogdanov, M.V. / Abdulmalik, O. / Han, L. / Tsai, A.L. / Idowu, M. / Juneja, H.S. / Kellems, R.E. / Dowhan, W. / Hansen, K.C. / Safo, M.K. / Xia, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ksj.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ksj.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ksj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ksj_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5ksj_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5ksj_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 5ksj_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/5ksj ftp://data.pdbj.org/pub/pdb/validation_reports/ks/5ksj | HTTPS FTP |
-Related structure data
Related structure data | 5ksiC 2dn2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | #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: 2.43 Å3/Da / Density % sol: 49.41 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.5 Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5 and 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 24236 / % possible obs: 96.6 % / Redundancy: 5.08 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.13 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.1 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DN2 Resolution: 2.4→30 Å / σ(F): 0 Details: Author provided the following evidence of direct S1P binding to hemoglobin: S1P beads successfully pulled down HbA from normal human erythrocyte lysates, while sphingosine or ...Details: Author provided the following evidence of direct S1P binding to hemoglobin: S1P beads successfully pulled down HbA from normal human erythrocyte lysates, while sphingosine or lysophosphatidic acid beads failed to pull down Hb. In addition, co-binding of 2,3-DPG and S1P to hemoglobin (Hb) is required for S1P-induced decrease in Hb-O2 affinity. We measured Oxygen Equilibration Curves (OEC) of purified HbA in the presence of 2,3-DPG along with S1P. We found that S1P decreased HbA-O2 binding affinity with increased P50 in a dose-dependent manner. Thus, we provide biochemical and functional evidence that S1P binds directly to Hb but requires cobinding of 2,3-DPG to decrease the protein affinity for O2
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Solvent computation | Bsol: 84.8405 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 100 Å2 / Biso mean: 43.7645 Å2 / Biso min: 4.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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