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- PDB-5f3h: Structure of myostatin in complex with humanized RK35 antibody -

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Basic information

Entry
Database: PDB / ID: 5f3h
TitleStructure of myostatin in complex with humanized RK35 antibody
Components
  • Growth/differentiation factor 8
  • humanized RK35 antibody heavy chain
  • humanized RK35 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 / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / negative regulation of satellite cell differentiation / 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 / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / negative regulation of satellite cell differentiation / 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: 2.7 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: humanized RK35 antibody heavy chain
B: humanized RK35 antibody light chain
C: humanized RK35 antibody heavy chain
D: humanized RK35 antibody light chain
E: humanized RK35 antibody heavy chain
F: humanized RK35 antibody light chain
G: humanized RK35 antibody heavy chain
H: humanized RK35 antibody light chain
I: Growth/differentiation factor 8
J: Growth/differentiation factor 8
K: Growth/differentiation factor 8
L: Growth/differentiation factor 8


Theoretical massNumber of molelcules
Total (without water)236,20512
Polymers236,20512
Non-polymers00
Water0
1
A: humanized RK35 antibody heavy chain
B: humanized RK35 antibody light chain
C: humanized RK35 antibody heavy chain
D: humanized RK35 antibody light chain
I: Growth/differentiation factor 8
J: Growth/differentiation factor 8


Theoretical massNumber of molelcules
Total (without water)118,1026
Polymers118,1026
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-97 kcal/mol
Surface area46350 Å2
MethodPISA
2
E: humanized RK35 antibody heavy chain
F: humanized RK35 antibody light chain
G: humanized RK35 antibody heavy chain
H: humanized RK35 antibody light chain
K: Growth/differentiation factor 8
L: Growth/differentiation factor 8


Theoretical massNumber of molelcules
Total (without water)118,1026
Polymers118,1026
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-96 kcal/mol
Surface area46470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.138, 80.916, 101.401
Angle α, β, γ (deg.)88.330, 103.780, 92.400
Int Tables number1
Space group name H-MP1
DetailsThis 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.

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Components

#1: Antibody
humanized RK35 antibody heavy chain


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
humanized RK35 antibody light chain


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
Growth/differentiation factor 8 / GDF-8 / Myostatin


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

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 40287

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F3B

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 2045 5.08 %RANDOM
Rwork0.2182 ---
obs0.2208 40287 63.5 %-
Displacement parametersBiso max: 148.52 Å2 / Biso mean: 39.13 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-7.9744 Å2-1.9888 Å214.3116 Å2
2---13.3077 Å25.5671 Å2
3---5.3334 Å2
Refine analyzeLuzzati coordinate error obs: 0.443 Å
Refinement stepCycle: final / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15915 0 0 0 15915
Num. residues----2099
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3715 51 5.54 %
Rwork0.3011 870 -
all0.3048 921 -
obs--63.5 %

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