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Yorodumi- PDB-3ikr: Crystal structure of alpha 1-4 mannobiose bound trimeric human lu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ikr | ||||||
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Title | Crystal structure of alpha 1-4 mannobiose bound trimeric human lung surfactant protein D | ||||||
Components | Pulmonary surfactant-associated protein D | ||||||
Keywords | SUGAR BINDING PROTEIN / Trimeric recombinant fragment / neck+CRD / Collagen / Disulfide bond / Extracellular matrix / Gaseous exchange / Glycoprotein / Hydroxylation / Lectin / Secreted / Surface film | ||||||
Function / homology | Function and homology information Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis / Signal regulatory protein family interactions / negative regulation of interleukin-2 production / lung alveolus development / macrophage chemotaxis / endocytic vesicle / negative regulation of T cell proliferation / positive regulation of phagocytosis / regulation of cytokine production / multivesicular body / reactive oxygen species metabolic process / receptor-mediated endocytosis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / SARS-CoV-1 activates/modulates innate immune responses / carbohydrate binding / lysosome / defense response to bacterium / innate immune response / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / isomorphous to native crystals / Resolution: 1.65 Å | ||||||
Authors | Shrive, A.K. / Greenhough, T.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325 Authors: Shrive, A.K. / Martin, C. / Burns, I. / Paterson, J.M. / Martin, J.D. / Townsend, J.P. / Waters, P. / Clark, H.W. / Kishore, U. / Reid, K.B.M. / Greenhough, T.J. #1: Journal: J.Mol.Biol. / Year: 2003 Title: High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D Authors: Shrive, A.K. / Tharia, H.A. / Strong, P. / Kishore, U. / Burns, I. / Rizkallah, P.J. / Reid, K.B.M. / Greenhough, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ikr.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ikr.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ikr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/3ikr ftp://data.pdbj.org/pub/pdb/validation_reports/ik/3ikr | HTTPS FTP |
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-Related structure data
Related structure data | 3iknC 3ikpC 3ikqC 1pw9S 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: 18834.957 Da / Num. of mol.: 3 / Fragment: UNP residues 199-375 / Mutation: P180S Source method: isolated from a genetically manipulated source Details: trimeric fragment comprising alpha helical neck region and carbohydrate recognition domains Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, PSPD, SFTP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35247 #2: Chemical | ChemComp-CA / #3: Sugar | #4: Water | ChemComp-HOH / | Nonpolymer details | THE CRYSTAL WAS SOAKED WITH ALPHA 1-4 MANNOBIOSE BUT ONLY ONE MANNOSE FROM THE MANNOBIOSE WAS SEEN ...THE CRYSTAL WAS SOAKED WITH ALPHA 1-4 MANNOBIOSE | |
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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: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 24, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→39.8 Å / Num. all: 74723 / Num. obs: 74723 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 7.6 / Num. unique all: 10101 / Rsym value: 0.151 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous to native crystals Starting model: 1pw9 Resolution: 1.65→39.79 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 34.712 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.59 Å2 / Biso mean: 21.233 Å2 / Biso min: 10.08 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→39.79 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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