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Yorodumi- PDB-1hup: HUMAN MANNOSE BINDING PROTEIN CARBOHYDRATE RECOGNITION DOMAIN TRI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hup | |||||||||
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Title | HUMAN MANNOSE BINDING PROTEIN CARBOHYDRATE RECOGNITION DOMAIN TRIMERIZES THROUGH A TRIPLE ALPHA-HELICAL COILED-COIL | |||||||||
Components | MANNOSE-BINDING PROTEIN | |||||||||
Keywords | C-TYPE LECTIN / ALPHA-HELICAL COILED-COIL | |||||||||
Function / homology | Function and homology information Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / negative regulation of viral process / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / serine-type endopeptidase complex ...Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / negative regulation of viral process / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / serine-type endopeptidase complex / Initial triggering of complement / D-mannose binding / positive regulation of phagocytosis / antiviral innate immune response / complement activation, classical pathway / multivesicular body / acute-phase response / calcium-dependent protein binding / response to oxidative stress / defense response to Gram-positive bacterium / defense response to bacterium / external side of plasma membrane / innate immune response / signaling receptor binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / proteolysis / extracellular space / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | |||||||||
Authors | Sheriff, S. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1994 Title: Human mannose-binding protein carbohydrate recognition domain trimerizes through a triple alpha-helical coiled-coil. Authors: Sheriff, S. / Chang, C.Y. / Ezekowitz, R.A. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Analysis of a Trimeric Form of Human Mannose Binding Protein Authors: Chang, C.Y. / Sastry, K.N. / Gillies, S.D. / Ezekowitz, R.A.B. / Sheriff, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hup.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hup.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hup_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 1hup_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 1hup_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1hup_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1hup ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1hup | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 193 | ||||||||||||
Components on special symmetry positions |
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Details | THE FOLLOWING TRANSFORMATIONS, WHEN APPLIED TO THE COORDINATES IN THIS ENTRY, WILL YIELD THE OTHER TWO MONOMERS OF THE TRIMER. SYMMETRY1 1 -0.499967 -0.866057 0.000000 38.33807 SYMMETRY2 1 0.865994 -0.500033 0.000000 -66.40547 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 2 -0.500033 0.866057 0.000000 76.68124 SYMMETRY2 2 -0.865994 -0.499967 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 |
-Components
#1: Protein | Mass: 15632.644 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: P11226 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.31 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Chang, C.Y., (1994) J.Mol.Biol., 241, 125. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 6978 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.088 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 22595 / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / σ(F): 1 /
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Displacement parameters | Biso mean: 30.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 807 /
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Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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