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Yorodumi- PDB-9c1a: Crystal structure of GDP-bound human M-RAS protein in crystal form I -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c1a | ||||||
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Title | Crystal structure of GDP-bound human M-RAS protein in crystal form I | ||||||
Components | Ras-related protein M-Ras | ||||||
Keywords | HYDROLASE / M-RAS / GDP / GTPase structure / RAS / crystal packing | ||||||
Function / homology | Function and homology information GTP-dependent protein binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / small monomeric GTPase / G protein activity / cellular response to leukemia inhibitory factor / RAF activation / GDP binding / actin cytoskeleton organization / Ras protein signal transduction ...GTP-dependent protein binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / small monomeric GTPase / G protein activity / cellular response to leukemia inhibitory factor / RAF activation / GDP binding / actin cytoskeleton organization / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Bester, S.M. / Abrahamsen, R. / Samora, L.R. / Wu, W.-I. / Mou, T.-C. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2024 Title: Crystal structure of the GDP-bound human M-RAS protein in two crystal forms. Authors: Bester, S.M. / Abrahamsen, R. / Rodrigues Samora, L. / Wu, W.I. / Mou, T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c1a.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c1a.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 9c1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c1a_validation.pdf.gz | 805.3 KB | Display | wwPDB validaton report |
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Full document | 9c1a_full_validation.pdf.gz | 805.4 KB | Display | |
Data in XML | 9c1a_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 9c1a_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/9c1a ftp://data.pdbj.org/pub/pdb/validation_reports/c1/9c1a | HTTPS FTP |
-Related structure data
Related structure data | 9c1bC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22253.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MRAS, RRAS3 / Production host: Escherichia coli (E. coli) / References: UniProt: O14807, small monomeric GTPase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-GDP / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M CaCl2, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→54.33 Å / Num. obs: 16016 / % possible obs: 94.03 % / Redundancy: 38.3 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 1 / Rpim(I) all: 0.032 / Rrim(I) all: 0.202 / Net I/σ(I): 19.82 |
Reflection shell | Resolution: 1.96→2.03 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1643 / CC1/2: 0.943 / Rpim(I) all: 0.293 / Rrim(I) all: 1.732 / % possible all: 99.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→54.33 Å / SU ML: 0.2004 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5772 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→54.33 Å
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Refine LS restraints |
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LS refinement shell |
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