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- PDB-3sek: Crystal Structure of the Myostatin:Follistatin-like 3 Complex -

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Basic information

Entry
Database: PDB / ID: 3sek
TitleCrystal Structure of the Myostatin:Follistatin-like 3 Complex
Components
  • Follistatin-related protein 3
  • Growth/differentiation factor 8
KeywordsSIGNALING PROTEIN / protein-protein complex / TB domain / cystine knot motif / TGF-beta fold / disulfide linked dimer / follistatin domain (FSD)
Function / homology
Function and homology information


negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway / 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 / Antagonism of Activin by Follistatin / skeletal muscle atrophy ...negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway / 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 / Antagonism of Activin by Follistatin / skeletal muscle atrophy / ovulation cycle process / regulation of BMP signaling pathway / response to gravity / positive regulation of cell-cell adhesion / skeletal muscle tissue regeneration / activin binding / negative regulation of activin receptor signaling pathway / negative regulation of myoblast differentiation / response to muscle activity / muscle cell cellular homeostasis / negative regulation of kinase activity / positive regulation of macrophage chemotaxis / response to testosterone / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / hematopoietic progenitor cell differentiation / positive regulation of lamellipodium assembly / response to electrical stimulus / negative regulation of insulin receptor signaling pathway / cellular response to dexamethasone stimulus / ossification / transforming growth factor beta receptor signaling pathway / cytokine activity / Post-translational protein phosphorylation / growth factor activity / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / heparin binding / cellular response to hypoxia / response to ethanol / cell differentiation / endoplasmic reticulum lumen / signaling receptor binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like ...Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Kazal type serine protease inhibitors / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Cystine-knot cytokine / Ribbon / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Growth/differentiation factor 8 / Follistatin-related protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.401 Å
AuthorsCash, J.N. / Thompson, T.B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of myostatinfollistatin-like 3: N-terminal domains of follistatin-type molecules exhibit alternate modes of binding.
Authors: Cash, J.N. / Angerman, E.B. / Kattamuri, C. / Nolan, K. / Zhao, H. / Sidis, Y. / Keutmann, H.T. / Thompson, T.B.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 21, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Growth/differentiation factor 8
C: Follistatin-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8773
Polymers34,6562
Non-polymers2211
Water1,06359
1
B: Growth/differentiation factor 8
C: Follistatin-related protein 3
hetero molecules

B: Growth/differentiation factor 8
C: Follistatin-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7546
Polymers69,3124
Non-polymers4422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area9730 Å2
ΔGint-68 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.086, 82.086, 312.691
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Growth/differentiation factor 8 / GDF-8 / Myostatin


Mass: 12422.212 Da / Num. of mol.: 1 / Fragment: UNP Residues 268-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gdf8, Mstn, myostatin / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O08689
#2: Protein Follistatin-related protein 3 / Follistatin-like protein 3 / Follistatin-related gene protein


Mass: 22233.553 Da / Num. of mol.: 1 / Fragment: UNP Residues 36-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLRG, follistatin-like 3, FSTL3, UNQ674/PRO1308 / Plasmid: pcDNA3.1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O95633
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7.5
Details: potassium thiocyanate, PEG 3350, pH 7.5, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 25404 / Num. obs: 25257 / % possible obs: 99.4 % / Observed criterion σ(I): 2.5 / Redundancy: 14.3 % / Rmerge(I) obs: 0.09 / Χ2: 1.203 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.495.20.70723791.165195.5
2.49-2.595.80.55224681.1991100
2.59-2.710.80.51424641.1951100
2.7-2.8516.90.48625141.251100
2.85-3.0217.90.3425031.3441100
3.02-3.2617.70.19325181.3261100
3.26-3.5817.60.11425361.2511100
3.58-4.117.50.08825881.2121100
4.1-5.17170.0626071.064199.9
5.17-5015.50.04728270.979198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3HH2 (chain B) and 3B4V (chain C)

3hh2

3b4v


Resolution: 2.401→35.54 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.701 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 1275 5.1 %RANDOM
Rwork0.2457 ---
obs0.2469 25168 98.85 %-
all-25168 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 183.9 Å2 / Biso mean: 69.9397 Å2 / Biso min: 31.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.401→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 14 59 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212416
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.9573289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6525308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2123.069101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5051519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211855
X-RAY DIFFRACTIONr_mcbond_it0.3941.51545
X-RAY DIFFRACTIONr_mcangle_it0.76422479
X-RAY DIFFRACTIONr_scbond_it1.2553871
X-RAY DIFFRACTIONr_scangle_it2.3024.5809
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 72 -
Rwork0.39 1600 -
all-1672 -
obs--92.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.84511.7189-3.0544.2952-4.366310.09560.15820.4555-0.09970.0694-0.16390.00520.3806-0.44480.00570.0949-0.0497-0.01370.4018-0.0320.3267-25.126428.697417.2944
24.9508-0.887-4.90711.3601-1.363710.3478-0.32340.0333-0.4-0.0808-0.5329-0.55630.81381.21710.85640.6651-0.10970.04780.58320.14710.7739-11.714115.79231.6618
37.1717-1.90110.13884.1078-2.11584.54750.21250.7098-0.0994-0.2259-0.14130.00580.05560.0033-0.07120.16050.05360.07130.65660.07080.3065-10.041535.309-1.496
414.14830.19221.54937.34070.28088.27620.16481.97441.7934-0.72270.11830.5994-0.9674-0.807-0.28310.46540.28490.07081.45550.65810.6184-24.615549.7657-12.9902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 109
2X-RAY DIFFRACTION2C10 - 105
3X-RAY DIFFRACTION3C106 - 181
4X-RAY DIFFRACTION4C182 - 218

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