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Yorodumi- PDB-5zm7: Crystal structure of ORP1-ORD in complex with cholesterol at 3.4 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zm7 | ||||||
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Title | Crystal structure of ORP1-ORD in complex with cholesterol at 3.4 A resolution | ||||||
Components | Oxysterol-binding protein-related protein 1 | ||||||
Keywords | LIPID TRANSPORT / Transporter / complex / lipid | ||||||
Function / homology | Function and homology information organelle membrane contact site / : / perinuclear endoplasmic reticulum / bile acid biosynthetic process / cholesterol binding / Synthesis of bile acids and bile salts / vesicle-mediated transport / MHC class II antigen presentation / cholesterol metabolic process / phospholipid binding ...organelle membrane contact site / : / perinuclear endoplasmic reticulum / bile acid biosynthetic process / cholesterol binding / Synthesis of bile acids and bile salts / vesicle-mediated transport / MHC class II antigen presentation / cholesterol metabolic process / phospholipid binding / late endosome / endosome / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.401 Å | ||||||
Authors | Dong, J. / Wang, J. / Wu, J.W. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P2/PI(3,4)P2. Authors: Dong, J. / Du, X. / Wang, H. / Wang, J. / Lu, C. / Chen, X. / Zhu, Z. / Luo, Z. / Yu, L. / Brown, A.J. / Yang, H. / Wu, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zm7.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zm7.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zm7_validation.pdf.gz | 634 KB | Display | wwPDB validaton report |
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Full document | 5zm7_full_validation.pdf.gz | 637.9 KB | Display | |
Data in XML | 5zm7_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 5zm7_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/5zm7 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/5zm7 | HTTPS FTP |
-Related structure data
Related structure data | 5zm5C 5zm6C 4ic4S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50528.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL1A, ORP1, OSBP8, OSBPL1, OSBPL1B / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BXW6 |
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#2: Chemical | ChemComp-CLR / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100mM Sodium acetate, pH 4.6, 2.0M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 8299 / % possible obs: 99.8 % / Redundancy: 17.9 % / Biso Wilson estimate: 116.9 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.018 / Rrim(I) all: 0.076 / Χ2: 1.421 / Net I/σ(I): 41.67 |
Reflection shell | Resolution: 3.401→3.52 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 8.11 / Num. unique obs: 793 / CC1/2: 0.964 / Rpim(I) all: 0.133 / Rrim(I) all: 0.565 / Χ2: 1.796 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IC4 Resolution: 3.401→36.199 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.401→36.199 Å
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Refine LS restraints |
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LS refinement shell |
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