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- PDB-1s4y: Crystal structure of the activin/actrIIb extracellular domain -

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Basic information

Entry
Database: PDB / ID: 1s4y
TitleCrystal structure of the activin/actrIIb extracellular domain
Components
  • Activin receptor type IIB precursor
  • Inhibin beta A chain
KeywordsTRANSFERASE / structural genomics / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


Signaling by Activin / 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 ...Signaling by Activin / 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 / Signaling by BMP / Antagonism of Activin by Follistatin / TGFBR3 regulates activin signaling / type II activin receptor binding / activin receptor activity, type II / progesterone secretion / lymphatic endothelial cell differentiation / Sertoli cell differentiation / striatal medium spiny neuron differentiation / positive regulation of activin receptor signaling pathway / enzyme activator complex / Glycoprotein hormones / negative regulation of macrophage differentiation / positive regulation of follicle-stimulating hormone secretion / negative regulation of phosphorylation / cellular response to oxygen-glucose deprivation / venous blood vessel development / hemoglobin biosynthetic process / lymphangiogenesis / testosterone biosynthetic process / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / cellular response to follicle-stimulating hormone stimulus / artery development / receptor protein serine/threonine kinase / cellular response to cholesterol / pattern specification process / activin binding / 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 / gastrulation with mouth forming second / mesodermal cell differentiation / pancreas development / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / odontogenesis / anterior/posterior pattern specification / negative regulation of cold-induced thermogenesis / insulin secretion / skeletal system morphogenesis / positive regulation of transcription by RNA polymerase III / organ growth / negative regulation of G1/S transition of mitotic cell cycle / growth factor binding / endodermal cell differentiation / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of protein metabolic process / mesoderm development / roof of mouth development / peptide hormone binding / negative regulation of type II interferon production / androgen metabolic process / cellular response to angiotensin / blood vessel remodeling / positive regulation of SMAD protein signal transduction / positive regulation of collagen biosynthetic process / hair follicle development / regulation of signal transduction / BMP signaling pathway / positive regulation of bone mineralization / response to glucose / positive regulation of osteoblast differentiation / hematopoietic progenitor cell differentiation / ovarian follicle development / extrinsic apoptotic signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of erythrocyte differentiation / erythrocyte differentiation / cytokine activity / skeletal system development / post-embryonic development / growth factor activity / kidney development / lung development / defense response / negative regulation of cell growth / hormone activity / autophagy / cytokine-mediated signaling pathway / male gonad development / nervous system development / cell-cell signaling / heart development / cellular response to hypoxia
Similarity search - Function
Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / 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 ...Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / 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 / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Inhibin beta A chain / Activin receptor type-2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGreenwald, J. / Vega, M.E. / Allendorph, G.P. / Fischer, W.H. / Vale, W. / Choe, S. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Mol.Cell / Year: 2004
Title: A Flexible Activin Explains the Membrane-Dependent Cooperative Assembly of TGF-beta Family Receptors.
Authors: Greenwald, J. / Vega, M.E. / Allendorph, G.P. / Fischer, W.H. / Vale, W. / Choe, S.
History
DepositionJan 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type IIB precursor
B: Inhibin beta A chain
C: Activin receptor type IIB precursor
D: Inhibin beta A chain


Theoretical massNumber of molelcules
Total (without water)49,1314
Polymers49,1314
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.290, 120.627, 43.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Activin receptor type IIB precursor / ACTR-IIB


Mass: 11573.676 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ACVR2B / Production host: Escherichia coli (E. coli) / References: UniProt: P27040, EC: 2.7.1.37
#2: 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: Cricetulus griseus (Chinese hamster) / References: UniProt: P08476
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 3350, magnesium chloride, bis tris, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 19028 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.047
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.213 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→70.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.367 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28615 988 5.2 %RANDOM
Rwork0.20611 ---
obs0.21021 18101 91.58 %-
all-18101 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 0 177 3279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0213195
X-RAY DIFFRACTIONr_bond_other_d0.0060.022606
X-RAY DIFFRACTIONr_angle_refined_deg2.3851.9284326
X-RAY DIFFRACTIONr_angle_other_deg1.10936090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2645385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023603
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02675
X-RAY DIFFRACTIONr_nbd_refined0.2190.2626
X-RAY DIFFRACTIONr_nbd_other0.2540.23072
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1030.21908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.2133
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3780.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.171.51946
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08623099
X-RAY DIFFRACTIONr_scbond_it3.37831249
X-RAY DIFFRACTIONr_scangle_it5.0374.51227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 69
Rwork0.222 1262
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.58250.8426-0.96676.798-1.30695.70080.1324-0.4428-0.15570.2414-0.195-0.49410.11040.7250.06270.03920.05420.05160.28760.05760.096330.719127.3673-1.8856
21.33980.1686-1.63450.19930.070910.48590.1986-0.20730.1110.2048-0.07310.0726-0.3839-0.1986-0.12540.1624-0.03690.02420.1430.0230.121612.859232.050217.3911
37.6593-0.16981.5677.89980.09464.43530.04690.4369-0.4348-0.23610.079-0.2023-0.0837-0.0132-0.12590.105-0.07540.03550.0762-0.0330.174731.341261.816327.092
410.80687.57384.86587.62293.24542.77520.0842-0.0390.2878-0.2309-0.0510.3190.0779-0.3463-0.03310.2827-0.0882-0.02310.28710.04670.234711.214547.615723.9236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 955 - 95
2X-RAY DIFFRACTION2BB2 - 1162 - 116
3X-RAY DIFFRACTION3CC4 - 984 - 98
4X-RAY DIFFRACTION4DD4 - 1164 - 116

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