+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37864 | |||||||||
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Title | C-reactive protein, pentamer | |||||||||
Map data | Relion postprocess sharpened map B factor = -136 | |||||||||
Sample |
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Keywords | Pentraxin / Immune System / Acute-phase reactant | |||||||||
Function / homology | Function and homology information regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / low-density lipoprotein particle receptor binding / Classical antibody-mediated complement activation / negative regulation of macrophage derived foam cell differentiation ...regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / low-density lipoprotein particle receptor binding / Classical antibody-mediated complement activation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of superoxide anion generation / acute-phase response / defense response to Gram-positive bacterium / inflammatory response / innate immune response / calcium ion binding / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Yadav S / Vinothkumar KR | |||||||||
Funding support | India, 2 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2024 Title: Factors affecting macromolecule orientations in thin films formed in cryo-EM. Authors: Swati Yadav / Kutti R Vinothkumar / Abstract: The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the ...The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37864.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-37864-v30.xml emd-37864.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37864_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_37864.png | 63 KB | ||
Filedesc metadata | emd-37864.cif.gz | 5.9 KB | ||
Others | emd_37864_half_map_1.map.gz emd_37864_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37864 | HTTPS FTP |
-Validation report
Summary document | emd_37864_validation.pdf.gz | 859.7 KB | Display | EMDB validaton report |
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Full document | emd_37864_full_validation.pdf.gz | 859.3 KB | Display | |
Data in XML | emd_37864_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_37864_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37864 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37864 | HTTPS FTP |
-Related structure data
Related structure data | 8wv4MC 8wv5C 8wv6C 8wzhC 8wziC 8wzjC 8wzkC 8wzmC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37864.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Relion postprocess sharpened map B factor = -136 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map from Relion
File | emd_37864_half_map_1.map | ||||||||||||
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Annotation | Half map from Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map from Relion
File | emd_37864_half_map_2.map | ||||||||||||
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Annotation | Half map from Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C-reactive protein purified from human serum with calcium
Entire | Name: C-reactive protein purified from human serum with calcium |
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Components |
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-Supramolecule #1: C-reactive protein purified from human serum with calcium
Supramolecule | Name: C-reactive protein purified from human serum with calcium type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 125 KDa |
-Macromolecule #1: C-reactive protein(1-205)
Macromolecule | Name: C-reactive protein(1-205) / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.061477 KDa |
Sequence | String: MEKLLCFLVL TSLSHAFGQT DMSRKAFVFP KESDTSYVSL KAPLTKPLKA FTVCLHFYTE LSSTRGYSIF SYATKRQDNE ILIFWSKDI GYSFTVGGSE ILFEVPEVTV APVHICTSWE SASGIVEFWV DGKPRVRKSL KKGYTVGAEA SIILGQEQDS F GGNFEGSQ ...String: MEKLLCFLVL TSLSHAFGQT DMSRKAFVFP KESDTSYVSL KAPLTKPLKA FTVCLHFYTE LSSTRGYSIF SYATKRQDNE ILIFWSKDI GYSFTVGGSE ILFEVPEVTV APVHICTSWE SASGIVEFWV DGKPRVRKSL KKGYTVGAEA SIILGQEQDS F GGNFEGSQ SLVGDIGNVN MWDFVLSPDE INTIYLGGPF SPNVLNWRAL KYEVQGEVFT KPQLWP UniProtKB: C-reactive protein |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 10 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.4 mg/mL | ||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force, 0. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 60.0 sec. / Average electron dose: 25.0 e/Å2 Details: Images were collected in movie mode (@40 fps) and total of 25 frames were saved. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 130841 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |