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- PDB-5hly: Structure of Pro-Activin A Precursor at 2.3 A Resolution -

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Basic information

Entry
Database: PDB / ID: 5hly
TitleStructure of Pro-Activin A Precursor at 2.3 A Resolution
ComponentsInhibin beta A chain
KeywordsSIGNALING PROTEIN / Growth factor / Precursor / Signalling
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. / 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: 2.302 Å
AuthorsWang, X. / Fischer, G. / Hyvonen, M.
CitationJournal: Nat Commun / Year: 2016
Title: Structure and activation of pro-activin A.
Authors: Wang, X. / Fischer, G. / Hyvonen, M.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 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 1.2Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6992
Polymers43,6641
Non-polymers351
Water45025
1
A: Inhibin beta A chain
hetero molecules

A: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3994
Polymers87,3282
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area5760 Å2
ΔGint-39 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.561, 46.561, 444.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 43664.020 Da / Num. of mol.: 1 / Mutation: C35S, C38S, deletion:K259-D282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Plasmid: pUBS520 / Details (production host): N-terminal His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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

CrystalDescription: rods
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% w/v polyethylene glycol 1000, 100 mM MES pH 6.5; cryo: 15% v/v PEG 400 added

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97866 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2014 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97866 Å / Relative weight: 1
ReflectionResolution: 2.3→74.15 Å / Num. obs: 11247 / % possible obs: 79.3 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 38.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rsym value: 0.114 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.4 / % possible all: 37.1

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2084: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: experimental phases from separate dataset

Resolution: 2.302→74.15 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 22.9 / Details: anomalous Se signal used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 977 5.17 %Random selection
Rwork0.2025 ---
obs0.2049 11167 79.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.07 Å2
Refinement stepCycle: LAST / Resolution: 2.302→74.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 1 25 2398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032424
X-RAY DIFFRACTIONf_angle_d0.7243262
X-RAY DIFFRACTIONf_dihedral_angle_d18.5341515
X-RAY DIFFRACTIONf_chiral_restr0.032362
X-RAY DIFFRACTIONf_plane_restr0.003419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3022-2.42360.2752790.25261206X-RAY DIFFRACTION38
2.4236-2.57550.4056940.25221616X-RAY DIFFRACTION50
2.5755-2.77430.28541330.24642195X-RAY DIFFRACTION69
2.7743-3.05350.24421860.21693146X-RAY DIFFRACTION98
3.0535-3.49540.24051730.20593248X-RAY DIFFRACTION100
3.4954-4.40370.24081540.17813252X-RAY DIFFRACTION100
4.4037-74.1920.2431580.19823260X-RAY DIFFRACTION100

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