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- PDB-5hlz: Structure of Pro-Activin A Complex at 2.85 A resolution -

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Basic information

Entry
Database: PDB / ID: 5hlz
TitleStructure of Pro-Activin A Complex at 2.85 A resolution
Components(Inhibin beta A chain) x 2
KeywordsSIGNALING PROTEIN / Growth factor / Precursor / Signalling
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. ...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
Inhibin beta A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.851 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inhibin beta A chain
B: Inhibin beta A chain
D: Inhibin beta A chain
F: Inhibin beta A chain
H: Inhibin beta A chain
C: Inhibin beta A chain
E: Inhibin beta A chain
G: Inhibin beta A chain


Theoretical massNumber of molelcules
Total (without water)173,0578
Polymers173,0578
Non-polymers00
Water18010
1
A: Inhibin beta A chain
B: Inhibin beta A chain
D: Inhibin beta A chain
C: Inhibin beta A chain


Theoretical massNumber of molelcules
Total (without water)86,5294
Polymers86,5294
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-80 kcal/mol
Surface area30340 Å2
MethodPISA
2
F: Inhibin beta A chain
H: Inhibin beta A chain
E: Inhibin beta A chain
G: Inhibin beta A chain


Theoretical massNumber of molelcules
Total (without water)86,5294
Polymers86,5294
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-79 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.227, 47.227, 445.425
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 30272.439 Da / Num. of mol.: 4 / Fragment: Pro domain, UNP Residues 30-305
Mutation: C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C ...Mutation: C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C protease cleavage site (LEVLFQGP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Details (production host): N-terminal His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476
#2: Protein
Inhibin beta A chain / Activin beta-A chain / Erythroid differentiation protein / EDF


Mass: 12991.865 Da / Num. of mol.: 4 / Fragment: Mature domain, UNP Residues 311-426
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 1.67 Å3/Da / Density % sol: 26.24 % / Description: Rods
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% w/v polyethylene glycol 3350, 0.2 M calcium chloride; cryo: 15% v/v PEG 400 added

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2014 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.85→44.54 Å / Num. obs: 26028 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rsym value: 0.141 / Net I/σ(I): 9.7
Reflection shellResolution: 2.85→3.01 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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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: Structure of the uncleaved growth factor

Resolution: 2.851→40.9 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.41 / Details: NCS restraint was included in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1331 5.14 %Random selection
Rwork0.2197 ---
obs0.2225 25879 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 69.62 Å2
Refinement stepCycle: LAST / Resolution: 2.851→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9153 0 0 10 9163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049318
X-RAY DIFFRACTIONf_angle_d0.8112536
X-RAY DIFFRACTIONf_dihedral_angle_d15.1075828
X-RAY DIFFRACTIONf_chiral_restr0.0381396
X-RAY DIFFRACTIONf_plane_restr0.0031605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8508-2.95270.39021380.32582541X-RAY DIFFRACTION100
2.9527-3.07090.34511440.28352326X-RAY DIFFRACTION100
3.0709-3.21060.31661390.27142518X-RAY DIFFRACTION100
3.2106-3.37980.30591400.2442516X-RAY DIFFRACTION100
3.3798-3.59140.29271230.22832408X-RAY DIFFRACTION100
3.5914-3.86850.29121310.20182446X-RAY DIFFRACTION100
3.8685-4.25750.2291240.19232486X-RAY DIFFRACTION100
4.2575-4.87270.22871310.17692418X-RAY DIFFRACTION100
4.8727-6.13570.25411390.20652438X-RAY DIFFRACTION100
6.1357-40.9040.27631220.23452451X-RAY DIFFRACTION98

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