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- PDB-2arp: Activin A in complex with Fs12 fragment of follistatin -

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Basic information

Entry
Database: PDB / ID: 2arp
TitleActivin A in complex with Fs12 fragment of follistatin
Components
  • Follistatin
  • Inhibin beta A chain
KeywordsHORMONE/GROWTH FACTOR / cystine knot / disulfide rich / egf domain / kazal domain / protein complex / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Antagonism of Activin by Follistatin / activin receptor antagonist activity / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin ...Antagonism of Activin by Follistatin / activin receptor antagonist activity / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion / type II activin receptor binding / striatal medium spiny neuron differentiation / ameloblast differentiation / Glycoprotein hormones / negative regulation of macrophage differentiation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / pattern specification process / Signaling by BMP / activin binding / activin receptor signaling pathway / negative regulation of phosphorylation / Signaling by Activin / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / heparan sulfate proteoglycan binding / cellular response to angiotensin / odontogenesis / positive regulation of transcription by RNA polymerase III / negative regulation of epithelial cell differentiation / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / female gonad development / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / odontogenesis of dentin-containing tooth / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / keratinocyte proliferation / hair follicle development / positive regulation of collagen biosynthetic process / BMP signaling pathway / hematopoietic progenitor cell differentiation / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / erythrocyte differentiation / positive regulation of erythrocyte differentiation / skeletal system development / cytokine activity / growth factor activity / response to organic cyclic compound / hormone activity / negative regulation of cell growth / cellular response to growth factor stimulus / defense response / cytokine-mediated signaling pathway / autophagy / male gonad development / cell-cell signaling / nervous system development / cellular response to hypoxia / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Follistatin, N-terminal / Inhibin, beta A subunit / 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 ...Follistatin, N-terminal / Inhibin, beta A subunit / 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 / Kazal domain superfamily / Transforming growth factor beta like domain / TGF-beta family profile. / Kazal domain / Kazal domain profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Cystine-knot cytokine / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / NICKEL (II) ION / Inhibin beta A chain / Follistatin
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHarrington, A.E. / Morris-Triggs, S.A. / Ruotolo, B.T. / Robinson, C.V. / Ohnuma, S. / Hyvonen, M.
CitationJournal: Embo J. / Year: 2006
Title: Structural basis for the inhibition of activin signalling by follistatin
Authors: Harrington, A.E. / Morris-Triggs, S.A. / Ruotolo, B.T. / Robinson, C.V. / Ohnuma, S. / Hyvonen, M.
History
DepositionAug 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inhibin beta A chain
F: Follistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,38210
Polymers29,5852
Non-polymers7978
Water3,081171
1
A: Inhibin beta A chain
F: Follistatin
hetero molecules

A: Inhibin beta A chain
F: Follistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,76420
Polymers59,1704
Non-polymers1,59416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10680 Å2
ΔGint-87 kcal/mol
Surface area28910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.297, 94.502, 44.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis: -X,-Y,Z.

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Components

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Protein , 2 types, 2 molecules AF

#1: Protein Inhibin beta A chain / Activin beta-A chain / Erythroid differentiation protein / EDF


Mass: 12991.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08476
#2: Protein Follistatin / FS / Activin-binding protein


Mass: 16593.193 Da / Num. of mol.: 1 / Fragment: Fs1-Fs2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fst / Plasmid: pHAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21674

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Non-polymers , 4 types, 179 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.9 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG-MME 2000, Nickel chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97926 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2→25.8 Å / Num. obs: 23201 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 32.33 Å2 / Rsym value: 0.055 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.67 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries: 1s4u, 1lr9

1s4u

1lr9


Resolution: 2→25.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.14 / SU ML: 0.108 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25404 1142 4.9 %RANDOM
Rwork0.20189 ---
all0.20189 23501 --
obs0.20189 22029 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.674 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.6 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 44 171 2160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222046
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9782747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79424.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53815360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.51511
X-RAY DIFFRACTIONr_chiral_restr0.1280.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021501
X-RAY DIFFRACTIONr_nbd_refined0.2770.2843
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.250.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3870.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.28
X-RAY DIFFRACTIONr_mcbond_it2.20521313
X-RAY DIFFRACTIONr_mcangle_it3.03132034
X-RAY DIFFRACTIONr_scbond_it2.4082850
X-RAY DIFFRACTIONr_scangle_it3.3213711
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 103 -
Rwork0.238 1590 -
obs--97.97 %

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