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- PDB-3b4v: X-Ray structure of Activin in complex with FSTL3 -

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Basic information

Entry
Database: PDB / ID: 3b4v
TitleX-Ray structure of Activin in complex with FSTL3
Components
  • Inhibin beta A chain
  • follistatin-like 3
KeywordsHORMONE REGULATOR COMPLEX / Ligand-inhibitor signalling complex / Cleavage on pair of basic residues / Glycoprotein / Growth factor / Hormone / Secreted / Nucleus / Proto-oncogene
Function / homology
Function and homology information


negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion ...negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / 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 / Glycoprotein hormones / negative regulation of macrophage differentiation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / positive regulation of cell-cell adhesion / regulation of BMP signaling pathway / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / Signaling by BMP / activin binding / activin receptor signaling pathway / negative regulation of phosphorylation / Signaling by Activin / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to angiotensin / odontogenesis / positive regulation of transcription by RNA polymerase III / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / negative regulation of osteoclast differentiation / peptide hormone binding / positive regulation of SMAD protein signal transduction / fibronectin binding / negative regulation of type II interferon production / negative regulation of BMP signaling pathway / 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 / ossification / erythrocyte differentiation / positive regulation of erythrocyte differentiation / cytokine activity / Post-translational protein phosphorylation / growth factor activity / hormone activity / negative regulation of cell growth / defense response / cytokine-mediated signaling pathway / autophagy / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / male gonad development / cell-cell signaling / nervous system development / cellular response to hypoxia / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / endoplasmic reticulum lumen / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Inhibin, beta A subunit / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal ...Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Inhibin, beta A subunit / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Kazal type serine protease inhibitors / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Kazal domain superfamily / Transforming growth factor beta like domain / TGF-beta family profile. / Kazal domain / Kazal domain profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Cystine-knot cytokine / Ribbon / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Follistatin-related protein 3 / Inhibin beta A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å
AuthorsThompson, T.B.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The structure of FSTL3.activin A complex. Differential binding of N-terminal domains influences follistatin-type antagonist specificity.
Authors: Stamler, R. / Keutmann, H.T. / Sidis, Y. / Kattamuri, C. / Schneyer, A. / Thompson, T.B.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
C: follistatin-like 3
D: follistatin-like 3
E: Inhibin beta A chain
F: Inhibin beta A chain
G: follistatin-like 3
H: follistatin-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,64614
Polymers151,9218
Non-polymers7256
Water3,189177
1
A: Inhibin beta A chain
B: Inhibin beta A chain
C: follistatin-like 3
D: follistatin-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4028
Polymers75,9604
Non-polymers4414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
MethodPISA
2
E: Inhibin beta A chain
F: Inhibin beta A chain
G: follistatin-like 3
H: follistatin-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2446
Polymers75,9604
Non-polymers2832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.613, 71.384, 100.203
Angle α, β, γ (deg.)98.55, 90.64, 90.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12C
22D
32G
42H
13B
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 116
2114E1 - 116
1124C6 - 218
2124D6 - 218
3124G6 - 218
4124H6 - 218
1134B1 - 116
2134F1 - 116

NCS ensembles :
ID
1
2
3
4
DetailsThe biological unit is a heterotetramer. There are 2 biological units in the asymmetric unit (chains A,B,C,D and chains E,F,G,H).

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Components

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Protein , 2 types, 8 molecules ABEFCDGH

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


Mass: 12991.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HEK293F / Gene: INHBA / Production host: Homo sapiens (human) / References: UniProt: P08476
#2: Protein
follistatin-like 3 / follistatin-related protein 3 / Follistatin-related gene protein


Mass: 24988.357 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HEK293F / Gene: FSTL3, FLRG / Production host: Homo sapiens (human) / References: UniProt: O95633

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Sugars , 1 types, 2 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 181 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.475→33.02 Å / Num. obs: 61295 / % possible obs: 98.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15
Reflection shellResolution: 2.48→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å31.79 Å
Translation4 Å31.79 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→31.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.741 / SU ML: 0.203 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27884 3144 5.1 %RANDOM
Rwork0.2266 ---
obs0.22926 58079 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.059 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.12 Å20.04 Å2
2--0.28 Å20.18 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.48→31.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9504 0 45 177 9726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9513168
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44951261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96223.2400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.766151531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4791574
X-RAY DIFFRACTIONr_chiral_restr0.0820.21427
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027434
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.23754
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.26558
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.43526513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.266310130
X-RAY DIFFRACTIONr_scbond_it1.64623722
X-RAY DIFFRACTIONr_scangle_it1.94633038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A845medium positional0.240.5
21C1486medium positional0.350.5
22D1486medium positional0.330.5
23G1486medium positional0.340.5
24H1486medium positional0.360.5
31B875medium positional0.270.5
11A845medium thermal1.2115
21C1486medium thermal5.1615
22D1486medium thermal5.1615
23G1486medium thermal4.9215
24H1486medium thermal5.0115
31B875medium thermal1.7815
LS refinement shellResolution: 2.475→2.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 205 -
Rwork0.313 3742 -
obs--86.41 %
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)
13.66540.01814.39660.9710.03188.5494-0.15790.10810.29040.0093-0.0212-0.0577-0.3790.30370.1791-0.2478-0.04230.0436-0.0466-0.0138-0.1046-12.7687-16.755738.0187
27.52822.10096.60871.52491.24366.1860.38470.0283-0.51760.2740.0117-0.23590.38980.1067-0.3964-0.216-0.0008-0.00130.05310.0123-0.157-17.1489-24.297739.7233
31.2145-0.59641.68070.5952-0.415512.26670.29740.1481-0.17720.04570.1234-0.12541.2560.8173-0.4208-0.09260.0532-0.0828-0.1173-0.0121-0.0497-6.4948-29.595748.4183
40.12670.05950.39490.5306-1.56117.29910.11940.142-0.13020.07010.1307-0.10320.0104-0.4881-0.2501-0.15810.0231-0.01990.02710.0154-0.0554-11.3788-22.686351.5551
52.90650.4158-4.44631.2878-0.44118.7235-0.2061-0.2218-0.2725-0.0268-0.0186-0.14320.5130.45090.2248-0.24740.0349-0.04030.016-0.006-0.1041-43.1465-14.342993.0632
69.8085-2.9152-7.45361.83721.95196.94740.52330.1210.4754-0.3506-0.1434-0.2768-0.46480.038-0.38-0.20270.02170.01850.01730.0505-0.1785-48.1165-6.712191.5634
71.58070.3948-1.51060.7408-0.228512.96760.1894-0.14890.2048-0.09490.0233-0.0986-1.37750.8041-0.2128-0.0878-0.06030.0731-0.1661-0.0282-0.0627-37.7804-1.41882.8391
80.7443-0.1780.85350.44-1.044110.5480.1465-0.14610.1774-0.1090.1216-0.077-0.1559-0.357-0.2681-0.1386-0.03190.0458-0.00720.0013-0.0557-42.7633-8.31679.8459
91.7883-2.93584.05515.7667-4.88289.48210.97310.3731-0.8452-0.69380.21020.75672.4272-0.114-1.18320.38550.0131-0.2636-0.0471-0.0460.51-20.5067-41.586732.2116
101.1464-0.70190.34831.87821.2066.89670.35190.0147-0.2637-0.0865-0.34760.47170.832-0.7217-0.00440.0929-0.0664-0.1028-0.28670.0392-0.0302-13.6816-33.700772.3504
118.7213-4.06072.902218.9881-0.81198.7637-0.13650.25911.1014-0.71390.2375-0.196-1.07610.3718-0.1010.0264-0.12690.038-0.26180.0969-0.053-8.9246-5.325459.7058
121.03330.49110.80273.21782.49334.21560.04190.06320.05870.19030.0713-0.1645-0.1619-0.1531-0.1132-0.21910.0131-0.0386-0.09010.0589-0.0925-35.9991-14.427929.6806
132.53553.6353-5.138118.4368-9.369710.71540.7999-0.28210.6290.89530.50120.5784-2.39040.0765-1.30110.4557-0.00720.3215-0.1401-0.04130.4025-51.353410.804799.3163
141.46640.4637-0.31832.63031.23756.35610.2709-0.0010.30260.1865-0.30050.4779-0.9183-0.67920.02960.20340.08060.0855-0.2550.0164-0.053-45.83092.817359.3084
153.98183.8679-1.540916.5238-1.094412.0068-0.3636-0.5096-0.98820.29910.1159-0.32331.24340.26940.2477-0.00040.13310.0934-0.16560.0950.0173-40.2235-25.755471.5083
160.9734-0.305-1.04683.6432.87024.634-0.0049-0.0603-0.0743-0.18930.0721-0.13140.1888-0.1162-0.0672-0.2340.00680.0128-0.11180.059-0.083-66.7922-16.5555101.6902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 664 - 66
2X-RAY DIFFRACTION2AA67 - 11667 - 116
3X-RAY DIFFRACTION3BB4 - 664 - 66
4X-RAY DIFFRACTION4BB67 - 11667 - 116
5X-RAY DIFFRACTION5EE4 - 664 - 66
6X-RAY DIFFRACTION6EE67 - 11667 - 116
7X-RAY DIFFRACTION7FF4 - 664 - 66
8X-RAY DIFFRACTION8FF67 - 11667 - 116
9X-RAY DIFFRACTION9CC11 - 6911 - 69
10X-RAY DIFFRACTION10CC70 - 8570 - 85
11X-RAY DIFFRACTION10CC87 - 21387 - 213
12X-RAY DIFFRACTION11DD10 - 3310 - 33
13X-RAY DIFFRACTION11DD35 - 6935 - 69
14X-RAY DIFFRACTION12DD70 - 21370 - 213
15X-RAY DIFFRACTION13GG11 - 5611 - 56
16X-RAY DIFFRACTION13GG58 - 6958 - 69
17X-RAY DIFFRACTION14GG70 - 21370 - 213
18X-RAY DIFFRACTION15HH10 - 3310 - 33
19X-RAY DIFFRACTION15HH35 - 6935 - 69
20X-RAY DIFFRACTION16HH70 - 21370 - 213

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