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Open data
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Basic information
Entry | Database: PDB / ID: 1b08 | ||||||
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Title | LUNG SURFACTANT PROTEIN D (SP-D) (FRAGMENT) | ||||||
![]() | PROTEIN (LUNG SURFACTANT PROTEIN D) | ||||||
![]() | SUGAR BINDING PROTEIN / C-TYPE LECTIN / CRD / SP-D / COLECTIN / ALPHA-HELICAL COILED-COIL / LUNG SURFACTANT | ||||||
Function / homology | ![]() Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / 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 ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / 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 / extracellular matrix organization / receptor-mediated endocytosis / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / collagen-containing extracellular matrix / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hakansson, K. / Lim, N.K. / Hoppe, H.-J. / Reid, K.B.M. | ||||||
![]() | ![]() Title: Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D. Authors: Hakansson, K. / Lim, N.K. / Hoppe, H.J. / Reid, K.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.9 KB | Display | ![]() |
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PDB format | ![]() | 80.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hupS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17055.906 Da / Num. of mol.: 3 Fragment: TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: AN EQUAL AMOUNT OF PROTEIN SOLUTION (8 MG/ML PROTEIN IN 10 MM TRIS 140 MM NACL 1MM CACL2 0.02% (W/V) NAN3 PH 7.5) AND PRECIPITANT BUFFER (10-20% (W/V) PEG 20000 IN 100 MM TRIS PH 6-8) WERE ...Details: AN EQUAL AMOUNT OF PROTEIN SOLUTION (8 MG/ML PROTEIN IN 10 MM TRIS 140 MM NACL 1MM CACL2 0.02% (W/V) NAN3 PH 7.5) AND PRECIPITANT BUFFER (10-20% (W/V) PEG 20000 IN 100 MM TRIS PH 6-8) WERE MIXED AND VAPOR EQUILIBRATED AGAINST THE LATTER., pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 28571 / % possible obs: 95 % / Redundancy: 2.45 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.29 / % possible all: 90.6 |
Reflection | *PLUS % possible obs: 95 % / Num. measured all: 69933 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 90.6 % / Num. unique obs: 2706 / Num. measured obs: 4769 / Mean I/σ(I) obs: 3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HUP Resolution: 2.3→20 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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