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Yorodumi- PDB-5zm5: Crystal structure of human ORP1-ORD in complex with cholesterol a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zm5 | ||||||
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Title | Crystal structure of human ORP1-ORD in complex with cholesterol at 2.6 A resolution | ||||||
Components | Oxysterol-binding protein-related protein 1 | ||||||
Keywords | LIPID TRANSPORT / Transporter / Complex | ||||||
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: 2.6 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 | 5zm5.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zm5.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zm5_validation.pdf.gz | 663.7 KB | Display | wwPDB validaton report |
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Full document | 5zm5_full_validation.pdf.gz | 666.5 KB | Display | |
Data in XML | 5zm5_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 5zm5_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/5zm5 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/5zm5 | HTTPS FTP |
-Related structure data
Related structure data | 5zm6C 5zm7C 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: 49981.016 Da / Num. of mol.: 1 / Fragment: UNP residues 534-950 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL1A / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BXW6 |
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#2: Chemical | ChemComp-CLR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 100mM Sodium Cacodylate, pH 6.2, 1.2M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97961 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97961 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 30261 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 41.72 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.038 / Rrim(I) all: 0.13 / Χ2: 1.232 / Net I/σ(I): 24.18 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 4.86 / Num. unique obs: 1478 / CC1/2: 0.927 / Rpim(I) all: 0.183 / Rrim(I) all: 0.644 / Χ2: 0.843 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IC4 Resolution: 2.6→39.954 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.954 Å
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Refine LS restraints |
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LS refinement shell |
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