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- PDB-6y6o: Structure of mature activin A with small molecule 42 -

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Basic information

Entry
Database: PDB / ID: 6y6o
TitleStructure of mature activin A with small molecule 42
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 / regulation of follicle-stimulating hormone secretion / negative regulation of B cell differentiation / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion ...activin A complex / inhibin A complex / cardiac fibroblast cell development / regulation of follicle-stimulating hormone secretion / negative regulation of B cell differentiation / 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 / negative regulation of macrophage differentiation / Glycoprotein hormones / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / Signaling by BMP / negative regulation of phosphorylation / activin receptor signaling pathway / Signaling by Activin / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / SMAD protein signal transduction / cellular response to angiotensin / positive regulation of transcription by RNA polymerase III / odontogenesis / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / endodermal cell differentiation / roof of mouth development / eyelid development in camera-type eye / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / hair follicle development / positive regulation of collagen biosynthetic process / hematopoietic progenitor cell differentiation / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / erythrocyte differentiation / positive regulation of erythrocyte differentiation / cytokine activity / growth factor activity / defense response / hormone activity / negative regulation of cell growth / autophagy / cytokine-mediated signaling pathway / male gonad development / cell-cell signaling / nervous system development / cellular response to hypoxia / transcription by RNA polymerase II / cell differentiation / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / 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 / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / 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
Chem-OCK / Inhibin beta A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsMcLoughlin, J.D. / Brear, P.B. / Reinhardt, T. / Spring, D.R. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chem Sci / Year: 2020
Title: Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion
Authors: Kidd, S.L. / Fowler, E. / Reinhardt, T. / Compton, T. / Mateu, N. / Newman, H. / Bellini, D. / Talon, R. / McLoughlin, J. / Krojer, T. / Aimon, A. / Bradley, A. / Fairhead, M. / Brear, P. / ...Authors: Kidd, S.L. / Fowler, E. / Reinhardt, T. / Compton, T. / Mateu, N. / Newman, H. / Bellini, D. / Talon, R. / McLoughlin, J. / Krojer, T. / Aimon, A. / Bradley, A. / Fairhead, M. / Brear, P. / Diaz-Saez, L. / McAuley, K. / Sore, H.F. / Madin, A. / O'Donovan, D.H. / Huber, K.V.M. / Hyvonen, M. / Dowson, C.G. / Spring, D.R.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 24, 2024Group: 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
A: Inhibin beta A chain
B: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7248
Polymers25,9842
Non-polymers7416
Water88349
1
A: Inhibin beta A chain
B: Inhibin beta A chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)53,44916
Polymers51,9674
Non-polymers1,48112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9230 Å2
ΔGint-209 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.050, 96.938, 117.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OCK / (3~{R})-4-ethyl-3-methyl-3-propyl-1~{H}-1,4-benzodiazepine-2,5-dione


Mass: 260.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.65 M (NH4)2SO4, 4 % PEG 300, 100 mM Hepes pH 7.4, 2 % DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97859 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97859 Å / Relative weight: 1
ReflectionResolution: 2.04→74.71 Å / Num. obs: 23146 / % possible obs: 97.2 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.069 / Rrim(I) all: 0.206 / Net I/σ(I): 8.7 / Num. measured all: 199275 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.04-2.158.92.89434320.4871.0083.068100
6.44-74.717.30.0638290.9980.0240.06899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2arv

2arv


Resolution: 2.04→74.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.238 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1118 4.9 %RANDOM
Rwork0.2233 ---
obs0.2248 21896 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.88 Å2 / Biso mean: 54.307 Å2 / Biso min: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.86 Å2-0 Å20 Å2
2---1.02 Å2-0 Å2
3---3.88 Å2
Refinement stepCycle: final / Resolution: 2.04→74.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 44 50 1869
Biso mean--69.54 45.92 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191882
X-RAY DIFFRACTIONr_bond_other_d0.0030.021689
X-RAY DIFFRACTIONr_angle_refined_deg2.1651.9422547
X-RAY DIFFRACTIONr_angle_other_deg1.16533911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4485225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26824.33783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13715313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.529156
X-RAY DIFFRACTIONr_chiral_restr0.130.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022120
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02440
LS refinement shellResolution: 2.04→2.089 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.431 77 -
Rwork0.406 1597 -
obs--96.26 %

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