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- PDB-5f3b: Structure of myostatin in complex with chimeric RK35 antibody -

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Basic information

Entry
Database: PDB / ID: 5f3b
TitleStructure of myostatin in complex with chimeric RK35 antibody
Components
  • Growth/differentiation factor 8
  • RK35 Chimeric antibody heavy chain
  • RK35 Chimeric antibody light chain
KeywordsSignaling 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 / negative regulation of satellite cell differentiation / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / skeletal muscle atrophy / 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 / negative regulation of satellite cell differentiation / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / skeletal muscle atrophy / 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
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Growth/differentiation factor 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsParris, K.D. / Mosyak, L.
CitationJournal: 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
DepositionDec 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RK35 Chimeric antibody heavy chain
B: RK35 Chimeric antibody light chain
E: RK35 Chimeric antibody heavy chain
F: RK35 Chimeric antibody light chain
C: Growth/differentiation factor 8
D: Growth/differentiation factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,33011
Polymers118,8696
Non-polymers4605
Water18,8621047
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-96 kcal/mol
Surface area48080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.090, 67.616, 78.559
Angle α, β, γ (deg.)78.980, 88.770, 67.440
Int Tables number1
Space group name H-MP1
DetailsMyostatin exists a dimer and one Fab (heavy/light chain pair) binds to each myostatin, so 6 polymers total.

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Components

#1: Antibody RK35 Chimeric antibody heavy chain


Mass: 23547.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody RK35 Chimeric antibody light chain


Mass: 23464.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Growth/differentiation factor 8 / GDF-8 / Myostatin


Mass: 12422.212 Da / Num. of mol.: 2 / Fragment: UNP residues 267-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSTN, GDF8 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O14793
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1047 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Chimeric RK35 Fab and myostatin were purified and the protein complex was concentrated to 10.75 mg/ml in a buffer of 50 mM tris hydrochloride pH 7.5 and 100 mM sodium chloride. Crystals were ...Details: Chimeric RK35 Fab and myostatin were purified and the protein complex was concentrated to 10.75 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 a solution containing 20% PEG MME 5000 and 100 mM bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→100 Å / Num. obs: 104791 / Redundancy: 1 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GCY

2gcy


Resolution: 1.76→49.17 Å / Cor.coef. Fo:Fc: 0.9406 / Cor.coef. Fo:Fc free: 0.9276 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 5240 5 %RANDOM
Rwork0.1794 ---
obs0.1807 104791 85.86 %-
Displacement parametersBiso max: 121.64 Å2 / Biso mean: 27.43 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1--5.5467 Å2-2.0072 Å24.7724 Å2
2--4.4801 Å23.6055 Å2
3---1.0666 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: final / Resolution: 1.76→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8174 0 30 1047 9251
Biso mean--39.82 36.85 -
Num. residues----1070
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3088 133 4.52 %
Rwork0.2771 2812 -
all0.2785 2945 -
obs--85.86 %

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