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Yorodumi- PDB-6z3h: Repulsive Guidance Molecule B (RGMB) in complex with Growth Diffe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z3h | ||||||||||||||||||||||||
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Title | Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 2) | ||||||||||||||||||||||||
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 mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation / mesenchymal cell apoptotic process / positive regulation of BMP signaling pathway ...ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation / mesenchymal cell apoptotic process / positive regulation of BMP signaling pathway / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / Molecules associated with elastic fibres / positive regulation of SMAD protein signal transduction / endoplasmic reticulum-Golgi intermediate compartment / 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 / cytokine activity / growth factor activity / negative regulation of epithelial cell proliferation / cell-cell signaling / negative regulation of neuron apoptotic process / cell adhesion / membrane raft / positive regulation of DNA-templated transcription / signal transduction / 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: 3.158 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 | 6z3h.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z3h.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 6z3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/6z3h ftp://data.pdbj.org/pub/pdb/validation_reports/z3/6z3h | HTTPS FTP |
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-Related structure data
Related structure data | 6z3gC 6z3jC 6z3lC 6z3mC 4ui0S C: citing same article (ref.) S: Starting model for refinement |
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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: 10532.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RGMB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6NW40 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M (NH4)2SO4, 0.1 M sodium acetate pH 4.6, 35% w/v pentaerythritol ethoxylate (15/4 EO/OH; average MW 797 Da) PH range: 4.6-8.0 |
-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: 3.13→64.98 Å / Num. obs: 5352 / % possible obs: 97.6 % / Redundancy: 35.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 3.13→3.21 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 380 / CC1/2: 0.806 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UI0 Resolution: 3.158→49.43 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.05 / 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: 3.158→49.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.158→49.43 Å
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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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