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- PDB-9i5w: Structure of mature Activin A from DMSO solvent optimisation of X... -

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Basic information

Entry
Database: PDB / ID: 9i5w
TitleStructure of mature Activin A from DMSO solvent optimisation of XChem fragment screen
ComponentsInhibin beta A chain
KeywordsSIGNALING PROTEIN / activin A / TGF-beta / growth factor / FBDD / inhibitor
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 / negative regulation of phosphorylation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / 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 / response to aldosterone / 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 / endodermal cell differentiation / eyelid development in camera-type eye / positive regulation of protein metabolic process / roof of mouth development / peptide hormone binding / negative regulation of type II interferon production / positive regulation of collagen biosynthetic process / androgen metabolic process / cellular response to angiotensin / positive regulation of SMAD protein signal transduction / hair follicle development / hematopoietic progenitor cell differentiation / ovarian follicle development / extrinsic apoptotic signaling pathway / positive regulation of erythrocyte differentiation / erythrocyte differentiation / cytokine activity / growth factor activity / defense response / negative regulation of cell growth / hormone activity / autophagy / male gonad development / cytokine-mediated signaling pathway / 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 / positive regulation of DNA-templated transcription / protein-containing complex binding / 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. / Cystine-knot cytokine
Similarity search - Domain/homology
Inhibin beta A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.774 Å
AuthorsQuambusch, L. / Hyvonen, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)505091675 Germany
CitationJournal: To Be Published
Title: Structure of mature Activin A
Authors: Quambusch, L. / Hyvonen, M.
History
DepositionJan 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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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)27,02914
Polymers25,9842
Non-polymers1,04512
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-87 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.791, 96.202, 118.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.55 M (NH4)2SO4, 100 mM Hepes pH 7.4, 8 % DMSO, 40 mM NaSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.774→74.76 Å / Num. obs: 22126 / % possible obs: 94.3 % / Redundancy: 11.6 % / Biso Wilson estimate: 33.95 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.6
Reflection shellResolution: 1.774→1.964 Å / Num. unique obs: 1106 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.774→48.1 Å / SU ML: 0.2145 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.1805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 1046 4.73 %
Rwork0.1983 21074 -
obs0.2001 22120 61.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.39 Å2
Refinement stepCycle: LAST / Resolution: 1.774→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 54 134 1934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741842
X-RAY DIFFRACTIONf_angle_d0.99012481
X-RAY DIFFRACTIONf_chiral_restr0.0589249
X-RAY DIFFRACTIONf_plane_restr0.0099315
X-RAY DIFFRACTIONf_dihedral_angle_d5.7911239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.774-1.870.3492170.3459313X-RAY DIFFRACTION6.58
1.87-1.990.3373460.2617951X-RAY DIFFRACTION19.77
1.99-2.140.25121060.24762099X-RAY DIFFRACTION43.73
2.14-2.350.25891760.24683339X-RAY DIFFRACTION69.14
2.35-2.690.27632160.2474403X-RAY DIFFRACTION91.03
2.69-3.390.25512500.21134897X-RAY DIFFRACTION100
3.39-48.10.20672350.16795072X-RAY DIFFRACTION99.98
Refinement TLS params.Method: refined / Origin x: -16.8092384556 Å / Origin y: -15.2565080352 Å / Origin z: -35.5631921215 Å
111213212223313233
T0.234958263623 Å20.0183484731401 Å20.0368083195937 Å2-0.190466204033 Å20.0751560969324 Å2--0.23681726158 Å2
L3.36743959589 °20.137301878673 °2-0.352188895935 °2-0.448780369912 °20.00643051893829 °2--0.164164415463 °2
S0.0984336764011 Å °0.272048134388 Å °0.578502724841 Å °-0.108461619422 Å °0.00122250353027 Å °0.0349179983627 Å °-0.163454199752 Å °-0.0368472186332 Å °-0.0566905884477 Å °
Refinement TLS groupSelection details: all

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