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Yorodumi- PDB-6z3g: Repulsive Guidance Molecule A (RGMA) in complex with Growth Diffe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z3g | ||||||||||||||||||||||||
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Title | Repulsive Guidance Molecule A (RGMA) in complex with Growth Differentiation Factor 5 (GDF5) | ||||||||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Repulsive Guidance Molecule / RGM / Bone Morphogenetic Protein / BMP / Growth Differentiation Factor 5 / GDF5 / Neogenin / axon guidance / TGFbeta signalling / brain development / iron metabolism. | ||||||||||||||||||||||||
Function / homology | Function and homology information ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation ...ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation / regulation of BMP signaling pathway / mesenchymal cell apoptotic process / transferrin receptor binding / positive regulation of BMP signaling pathway / negative regulation of chondrocyte differentiation / positive regulation of membrane protein ectodomain proteolysis / embryonic limb morphogenesis / Molecules associated with elastic fibres / positive regulation of SMAD protein signal transduction / membrane protein ectodomain proteolysis / regulation of multicellular organism growth / chondrocyte differentiation / BMP signaling pathway / coreceptor activity / side of membrane / response to mechanical stimulus / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / neural tube closure / cytokine activity / growth factor activity / positive regulation of neuron projection development / negative regulation of epithelial cell proliferation / neuron projection development / cell-cell signaling / negative regulation of neuron apoptotic process / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||||||||||||||||||||
Authors | Malinauskas, T. / Peer, T.V. / Bishop, B. / Muller, T.D. / Siebold, C. | ||||||||||||||||||||||||
Funding support | United Kingdom, Germany, 7items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Repulsive guidance molecules lock growth differentiation factor 5 in an inhibitory complex. Authors: Malinauskas, T. / Peer, T.V. / Bishop, B. / Mueller, T.D. / Siebold, C. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z3g.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z3g.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 6z3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z3g_validation.pdf.gz | 629.3 KB | Display | wwPDB validaton report |
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Full document | 6z3g_full_validation.pdf.gz | 631.7 KB | Display | |
Data in XML | 6z3g_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 6z3g_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/6z3g ftp://data.pdbj.org/pub/pdb/validation_reports/z3/6z3g | HTTPS FTP |
-Related structure data
Related structure data | 6z3hC 6z3jC 6z3lC 6z3mC 4uhyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13405.481 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GDF5, BMP14, CDMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43026 |
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#2: Protein | Mass: 11628.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RGMA, RGM / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96B86 |
#3: Chemical | ChemComp-CIT / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.5, 24% v/v polyethylene glycol (PEG) 400. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→49.91 Å / Num. obs: 7375 / % possible obs: 97.8 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.78→2.85 Å / Rmerge(I) obs: 4.129 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 494 / CC1/2: 0.592 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UHY Resolution: 2.78→48.825 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→48.825 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 |
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