+Open data
-Basic information
Entry | Database: PDB / ID: 5f3h | ||||||
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Title | Structure of myostatin in complex with humanized RK35 antibody | ||||||
Components |
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Keywords | Signaling Protein/Immune System / myostatin / antibody / complex / Signaling Protein-Immune System complex | ||||||
Function / homology | Function and homology information negative regulation of muscle hypertrophy / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / skeletal muscle satellite cell differentiation / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / skeletal muscle atrophy / negative regulation of satellite cell differentiation / ovulation cycle process / FOXO-mediated transcription of cell cycle genes ...negative regulation of muscle hypertrophy / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / skeletal muscle satellite cell differentiation / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / skeletal muscle atrophy / negative regulation of satellite cell differentiation / ovulation cycle process / FOXO-mediated transcription of cell cycle genes / response to gravity / negative regulation of myoblast differentiation / response to muscle activity / muscle organ development / muscle cell cellular homeostasis / positive regulation of macrophage chemotaxis / response to testosterone / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of lamellipodium assembly / response to electrical stimulus / negative regulation of insulin receptor signaling pathway / cellular response to dexamethasone stimulus / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / response to estrogen / heparin binding / cellular response to hypoxia / response to ethanol / signaling receptor binding / positive regulation of DNA-templated transcription / protein homodimerization activity / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Parris, K.D. / Mosyak, L. | ||||||
Citation | Journal: Mabs / Year: 2016 Title: Beyond CDR-grafting: Structure-guided humanization of framework and CDR regions of an anti-myostatin antibody. Authors: Apgar, J.R. / Mader, M. / Agostinelli, R. / Benard, S. / Bialek, P. / Johnson, M. / Gao, Y. / Krebs, M. / Owens, J. / Parris, K. / St Andre, M. / Svenson, K. / Morris, C. / Tchistiakova, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f3h.cif.gz | 394.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f3h.ent.gz | 322.5 KB | Display | PDB format |
PDBx/mmJSON format | 5f3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f3h ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f3h | HTTPS FTP |
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-Related structure data
Related structure data | 5f3bSC 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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2 |
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Unit cell |
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Details | This structure contains two biological assemblies. Myostatin is a dimer in solution. Each Myostatin monomer is in complex with RK35 Fab Heavy and Light chains. Thus in this structure one assembly is chains A/B/C/D/I/J the second assembly is E/F/G/H/K/L. |
-Components
#1: Antibody | Mass: 23369.123 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 23374.879 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) #3: Protein | Mass: 12307.124 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MSTN, GDF8 / Production host: Cricetus (mammal) / References: UniProt: O14793 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Humanized RK35 Fab and myostatin were purified and the protein complex was concentrated to 10 mg/ml in a buffer of 50 mM tris hydrochloride pH 7.5 and 100 mM sodium chloride. Crystals were ...Details: Humanized RK35 Fab and myostatin were purified and the protein complex was concentrated to 10 mg/ml in a buffer of 50 mM tris hydrochloride pH 7.5 and 100 mM sodium chloride. Crystals were obtained using the hanging drop method with equilibration at 18C against an unbuffered solution containing 20% PEG 3350 and 200mM sodium chloride. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 40287 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F3B Resolution: 2.7→19.99 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.7929 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.504
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Displacement parameters | Biso max: 148.52 Å2 / Biso mean: 39.13 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.443 Å | ||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→19.99 Å
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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