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Open data
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Basic information
Entry | Database: PDB / ID: 8ivd | ||||||
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Title | COMPLEX STRUCTURE OF CD93-IGFBP7 | ||||||
![]() | Insulin-like growth factor-binding protein 7,Complement component C1q receptor | ||||||
![]() | CELL ADHESION / Complex structure / immune regulation / adhesion / tumor suppression | ||||||
Function / homology | ![]() response to cortisol / regulation of steroid biosynthetic process / complement component C1q complex binding / insulin-like growth factor binding / macrophage activation / tertiary granule membrane / ficolin-1-rich granule membrane / regulation of signal transduction / specific granule membrane / phagocytosis ...response to cortisol / regulation of steroid biosynthetic process / complement component C1q complex binding / insulin-like growth factor binding / macrophage activation / tertiary granule membrane / ficolin-1-rich granule membrane / regulation of signal transduction / specific granule membrane / phagocytosis / response to retinoic acid / cellular response to hormone stimulus / embryo implantation / secretory granule membrane / regulation of cell growth / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / signaling receptor activity / Senescence-Associated Secretory Phenotype (SASP) / carbohydrate binding / collagen-containing extracellular matrix / membrane => GO:0016020 / cell adhesion / negative regulation of cell population proliferation / endoplasmic reticulum lumen / calcium ion binding / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, Y.M. / Song, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: structural insight into CD93 recognition by IGFBP7 Authors: Xu, Y.M. / Song, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 360 KB | Display | ![]() |
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PDB format | ![]() | 241.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.9 KB | Display | ![]() |
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Full document | ![]() | 480.1 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50329.371 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The depositor stated, 'for the large gap, we agree that the distance between C-ter of chainC and N-ter of Chain B is too large (~60 A) that the linker can not cover the gap, that's why we ...Details: The depositor stated, 'for the large gap, we agree that the distance between C-ter of chainC and N-ter of Chain B is too large (~60 A) that the linker can not cover the gap, that's why we doubt that these two are in a single chain and Chain C is possible to linker to chainA as their distance is ~12A. As this is not conclusive since the densities for linker are missing i suggest we name these chains (A-D) individually as i submitted, and this numbering method has been used by many other researcher, and will benefit the reader (as the numbering will be consistent with their nature numbering).' Source: (gene. exp.) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M imidazole, 20% w/v PEG monomethyl ether 2000, and 0.2 M ammonium citrate tribasic pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2022 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.24→48.2 Å / Num. obs: 17340 / % possible obs: 99.9 % / Redundancy: 12 % / Biso Wilson estimate: 118.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.09 / Rrim(I) all: 0.2 / Rsym value: 0.2 / Χ2: 0.99 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.24→3.5 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.14 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3495 / CC1/2: 0.48 / Rpim(I) all: 1 / Χ2: 1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 143.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.24→19.95 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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