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- PDB-7oly: Structure of activin A in complex with an ActRIIB-Alk4 fusion rev... -

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Basic information

Entry
Database: PDB / ID: 7oly
TitleStructure of activin A in complex with an ActRIIB-Alk4 fusion reveal insight into activin receptor interactions
Components
  • (Activin receptor type- ...) x 2
  • Fab heavy chain
  • Fab light chain
  • Inhibin beta A chain
KeywordsSIGNALING PROTEIN / GROWTH FACTOR / RECEPTOR / TGFB / SIGNALING
Function / homology
Function and homology information


inhibin binding / activin A complex / inhibin A complex / cardiac fibroblast cell development / Regulation of signaling by NODAL / 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 ...inhibin binding / activin A complex / inhibin A complex / cardiac fibroblast cell development / Regulation of signaling by NODAL / 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 receptor activity / TGFBR3 regulates activin signaling / type II activin receptor binding / progesterone secretion / activin receptor activity, type II / Sertoli cell differentiation / lymphatic endothelial cell differentiation / striatal medium spiny neuron differentiation / nodal signaling pathway / positive regulation of activin receptor signaling pathway / Glycoprotein hormones / enzyme activator complex / negative regulation of macrophage differentiation / negative regulation of phosphorylation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / venous blood vessel development / hemoglobin biosynthetic process / lymphangiogenesis / trophoblast cell migration / testosterone biosynthetic process / positive regulation of trophoblast cell migration / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex / cellular response to follicle-stimulating hormone stimulus / activin receptor activity, type I / artery development / transmembrane receptor protein serine/threonine kinase activity / cellular response to cholesterol / receptor protein serine/threonine kinase / activin binding / pattern specification process / SMAD protein signal transduction / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / Signaling by NODAL / response to aldosterone / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / gastrulation with mouth forming second / pancreas development / I-SMAD binding / mesodermal cell differentiation / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / odontogenesis / anterior/posterior pattern specification / negative regulation of cold-induced thermogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / insulin secretion / skeletal system morphogenesis / positive regulation of transcription by RNA polymerase III / organ growth / growth factor binding / negative regulation of G1/S transition of mitotic cell cycle / SMAD binding / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / endodermal cell differentiation / mesoderm development / positive regulation of protein metabolic process / roof of mouth development / peptide hormone binding / negative regulation of type II interferon production / positive regulation of collagen biosynthetic process / androgen metabolic process / cellular response to angiotensin / positive regulation of SMAD protein signal transduction / peptidyl-threonine phosphorylation / blood vessel remodeling / negative regulation of cell differentiation / hair follicle development / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to glucose / BMP signaling pathway / hematopoietic progenitor cell differentiation / ovarian follicle development / extrinsic apoptotic signaling pathway / protein serine/threonine/tyrosine kinase activity / lung development / positive regulation of erythrocyte differentiation / cytokine activity / erythrocyte differentiation / post-embryonic development / growth factor activity
Similarity search - Function
Inhibin, beta A subunit / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / Activin types I and II receptor domain ...Inhibin, beta A subunit / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / Activin types I and II receptor domain / 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. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Inhibin beta A chain / Activin receptor type-1B / Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.265 Å
AuthorsHakansson, M. / Rose, N.C. / Castonguay, R. / Logan, D.T. / Krishnan, L.
CitationJournal: Iscience / Year: 2022
Title: Structures of activin ligand traps using natural sets of type I and type II TGF beta receptors.
Authors: Goebel, E.J. / Kattamuri, C. / Gipson, G.R. / Krishnan, L. / Chavez, M. / Czepnik, M. / Maguire, M.C. / Grenha, R. / Hakansson, M. / Logan, D.T. / Grinberg, A.V. / Sako, D. / Castonguay, R. ...Authors: Goebel, E.J. / Kattamuri, C. / Gipson, G.R. / Krishnan, L. / Chavez, M. / Czepnik, M. / Maguire, M.C. / Grenha, R. / Hakansson, M. / Logan, D.T. / Grinberg, A.V. / Sako, D. / Castonguay, R. / Kumar, R. / Thompson, T.B.
History
DepositionMay 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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
C: Activin receptor type-2B
H: Fab heavy chain
K: Activin receptor type-1B
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3607
Polymers89,0255
Non-polymers1,3352
Water27015
1
A: Inhibin beta A chain
C: Activin receptor type-2B
H: Fab heavy chain
K: Activin receptor type-1B
L: Fab light chain
hetero molecules

A: Inhibin beta A chain
C: Activin receptor type-2B
H: Fab heavy chain
K: Activin receptor type-1B
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,72014
Polymers178,04910
Non-polymers2,6704
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Unit cell
Length a, b, c (Å)68.375, 68.375, 975.538
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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Components

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Activin receptor type- ... , 2 types, 2 molecules CK

#2: Protein Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 14933.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B / Cell line (production host): CHO / Production host: Homo sapiens (human)
References: UniProt: Q13705, receptor protein serine/threonine kinase
#4: Protein Activin receptor type-1B / Activin receptor type IB / ACTR-IB / Activin receptor-like kinase 4 / ALK-4 / Serine/threonine- ...Activin receptor type IB / ACTR-IB / Activin receptor-like kinase 4 / ALK-4 / Serine/threonine-protein kinase receptor R2 / SKR2


Mass: 13122.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1B, ACVRLK4, ALK4 / Cell line (production host): CHO / Production host: Homo sapiens (human)
References: UniProt: P36896, receptor protein serine/threonine kinase

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab heavy chain


Mass: 23772.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Homo sapiens (human)
#5: Antibody Fab light chain


Mass: 24203.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 16 molecules A

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


Mass: 12991.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Cell line (production host): CHO / Production host: Homo sapiens (human) / References: UniProt: P08476
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-6DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-1/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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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Details

Has ligand of interestN
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: 3.7 Å3/Da / Density % sol: 66.73 % / Description: Disc-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17.7 mg/ml complex in 20 mM HEPES, 200 mM NaCl pH 7.5. 100 + 100 nl sitting drop in a MRC 3-well plate with reservoir 0.1 M Na cacodylate pH 6.5 and 17 % (w/v) PEG 4000).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.992 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 3.26→49.25 Å / Num. obs: 23230 / % possible obs: 99.9 % / Redundancy: 35.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.054 / Net I/σ(I): 11.7
Reflection shellResolution: 3.26→3.39 Å / Rmerge(I) obs: 2.667 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4489 / CC1/2: 0.504 / Rpim(I) all: 0.446 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MxCuBEdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K59, 5MAC, 2ARV

5k59

5mac

2arv


Resolution: 3.265→49.25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 5.022 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.449 / SU Rfree Cruickshank DPI: 0.436
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 1209 -RANDOM
Rwork0.2344 ---
obs0.2362 23004 99.7 %-
Displacement parametersBiso mean: 112.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.9125 Å20 Å20 Å2
2--2.9125 Å20 Å2
3----5.825 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 3.265→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 0 89 15 5718
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085859HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.997982HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1981SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes977HARMONIC5
X-RAY DIFFRACTIONt_it5859HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion790SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3999SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion20.35
LS refinement shellResolution: 3.27→3.29 Å
RfactorNum. reflection% reflection
Rfree0.483 30 -
Rwork0.3824 --
obs0.3884 461 86.57 %
Refinement TLS params.

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)
11.54220.61970.64792.447-1.22251.46010.13060.11180.02940.1118-0.04550.01390.02940.0139-0.08511.1837-0.15820.01630.9573-0.0730.9079-16.72187.9556-73.5315
21.44881.06830.43174.2768-0.78814.64080.0743-0.36020.0431-0.3602-0.16510.03040.04310.03040.09081.3271-0.1864-0.0821.07670.09420.9393-7.5935-11.2914-54.4596
33.6148-0.72080.98883.3226-0.64700.23040.017-0.36450.017-0.17950.0055-0.36450.0055-0.05091.2215-0.09320.03091.1077-0.05251.125-27.3342-12.4998-84.7718
41.5078-0.26010.53121-0.77843.1673-0.0831-0.16460.2715-0.16460.0477-0.14520.2715-0.14520.03540.7736-0.10250.08170.47350.03660.94816.3361-25.221-22.9498
51.4023-0.46181.26051.3327-0.58493.1053-0.2265-0.0773-0.2106-0.07730.1320.145-0.21060.1450.09450.7911-0.06990.10830.580.15560.985816.0054-12.2043-15.9897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|311 - A|426 }A311 - 426
2X-RAY DIFFRACTION2{ C|26 - C|120 }C26 - 120
3X-RAY DIFFRACTION2{ C|701 - C|701 }C701
4X-RAY DIFFRACTION3{ K|31 - K|109 }K31 - 109
5X-RAY DIFFRACTION4{ H|1 - H|219 }H1 - 219
6X-RAY DIFFRACTION5{ L|1 - L|220 }L1 - 220

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