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- PDB-2arv: Structure of human Activin A -

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Basic information

Entry
Database: PDB / ID: 2arv
TitleStructure of human Activin A
ComponentsInhibin beta A chain
KeywordsHORMONE/GROWTH FACTOR / homodimer / cystine knot / disulfide linked / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


activin A complex / inhibin A complex / cardiac fibroblast cell development / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / negative regulation of follicle-stimulating hormone secretion / GABAergic neuron differentiation / Antagonism of Activin by Follistatin ...activin A complex / inhibin A complex / cardiac fibroblast cell development / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / negative regulation of follicle-stimulating hormone secretion / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / TGFBR3 regulates activin signaling / type II activin receptor binding / progesterone secretion / Sertoli cell differentiation / striatal medium spiny neuron differentiation / enzyme activator complex / Glycoprotein hormones / negative regulation of macrophage differentiation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / negative regulation of phosphorylation / testosterone biosynthetic process / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / SMAD protein signal transduction / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / mesodermal cell differentiation / odontogenesis / positive regulation of transcription by RNA polymerase III / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / endodermal cell differentiation / eyelid development in camera-type eye / roof of mouth development / negative regulation of type II interferon production / peptide hormone binding / positive regulation of protein metabolic process / androgen metabolic process / positive regulation of collagen biosynthetic process / positive regulation of SMAD protein signal transduction / cellular response to angiotensin / hair follicle development / hematopoietic progenitor cell differentiation / ovarian follicle development / extrinsic apoptotic signaling pathway / erythrocyte differentiation / positive regulation of erythrocyte differentiation / cytokine activity / growth factor activity / defense response / negative regulation of cell growth / cytokine-mediated signaling pathway / hormone activity / autophagy / male gonad development / nervous system development / cell-cell signaling / cellular response to hypoxia / transcription by RNA polymerase II / cell differentiation / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / negative regulation of cell population proliferation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein-containing complex binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Inhibin, beta A subunit / 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. ...Inhibin, beta A subunit / 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 / Mainly Beta
Similarity search - Domain/homology
Chem-1PG / Inhibin beta A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
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 22, 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: Non-polymer description / 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibin beta A chain
B: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,89710
Polymers25,9842
Non-polymers9138
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-65 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.572, 96.247, 118.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 1 - 116 / Label seq-ID: 1 - 116

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA
DetailsThe biological unit is a homodimer as found in the asymmetric unit

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Components

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


Mass: 12991.865 Da / Num. of mol.: 2
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulphate, PEG300, Na-Hepes, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978847 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: 0.978847 Å / Relative weight: 1
ReflectionResolution: 2→29.2 Å / Num. obs: 24229 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.065

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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 entry 1S4Y

1s4y


Resolution: 2→29.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.949 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1151 4.9 %RANDOM
Rwork0.2159 ---
all0.21802 22157 --
obs0.21802 22157 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.624 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---0.07 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 2→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 55 54 1853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211858
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9562503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93124.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.98315308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.176156
X-RAY DIFFRACTIONr_chiral_restr0.1350.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021380
X-RAY DIFFRACTIONr_nbd_refined0.2710.2704
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.26
X-RAY DIFFRACTIONr_mcbond_it6.51121134
X-RAY DIFFRACTIONr_mcangle_it7.93531780
X-RAY DIFFRACTIONr_scbond_it7.9662833
X-RAY DIFFRACTIONr_scangle_it10.0483722
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 829 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.880.5
medium thermal8.372
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 64 -
Rwork0.255 1350 -
obs--78.56 %

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