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- PDB-6y6n: Structure of mature activin A with small molecule 2 -

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Basic information

Entry
Database: PDB / ID: 6y6n
TitleStructure of mature activin A with small molecule 2
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 / enzyme activator complex / regulation of follicle-stimulating hormone secretion / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / positive regulation of ovulation / negative regulation of follicle-stimulating hormone secretion / GABAergic neuron differentiation ...activin A complex / inhibin A complex / cardiac fibroblast cell development / enzyme activator complex / regulation of follicle-stimulating hormone secretion / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / 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 / 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 / activin receptor signaling pathway / Signaling by Activin / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / mesodermal cell differentiation / odontogenesis / positive regulation of transcription by RNA polymerase III / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / peptide hormone binding / negative regulation of type II interferon production / 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 / positive regulation of protein metabolic process / positive regulation of erythrocyte differentiation / erythrocyte differentiation / cytokine activity / growth factor activity / defense response / negative regulation of cell growth / hormone activity / cytokine-mediated signaling pathway / autophagy / 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 / 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. / Cystine-knot cytokine
Similarity search - Domain/homology
Chem-ODQ / Inhibin beta A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)26,6147
Polymers25,9842
Non-polymers6315
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Disulfide-linked dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-70 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.253, 96.951, 120.270
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 / Details (production host): pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476
#2: Chemical ChemComp-ODQ / (3~{R})-3,4-dimethyl-3-propyl-1~{H}-1,4-benzodiazepine-2,5-dione


Mass: 246.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.6 Å3/Da / Density % sol: 65.87 %
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: 0.97858 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 2.03→56.67 Å / Num. obs: 24727 / % possible obs: 99.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 42.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.065 / Rrim(I) all: 0.194 / Net I/σ(I): 8.3 / Num. measured all: 214143 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.148.92.76435640.4870.9642.932100
6.41-56.677.30.0658650.9960.0250.0799.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2arv

2arv


Resolution: 2.03→22.54 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1160 5.04 %RANDOM
Rwork0.236 ---
obs0.236 23023 93.4 %-
Displacement parametersBiso max: 164.99 Å2 / Biso mean: 55.62 Å2 / Biso min: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.1411 Å20 Å20 Å2
2--3.7475 Å20 Å2
3----13.8886 Å2
Refinement stepCycle: final / Resolution: 2.03→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 38 43 1835
Biso mean--86.69 53 -
Num. residues----223
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d625SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes271HARMONIC5
X-RAY DIFFRACTIONt_it1843HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion230SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1973SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1843HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2494HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion20.84
LS refinement shellResolution: 2.03→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2407 135 4.76 %
Rwork0.2396 2704 -
all0.2397 2839 -
obs--96.1 %

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