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- PDB-7u5p: CRYSTAL STRUCTURE OF THE ACTIVIN RECEPTOR TYPE-2A LIGAND BINDING ... -

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Basic information

Entry
Database: PDB / ID: 7u5p
TitleCRYSTAL STRUCTURE OF THE ACTIVIN RECEPTOR TYPE-2A LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-A
Components
  • Activin receptor type-2A
  • Inhibin beta A chain
KeywordsSIGNALING PROTEIN / Cell Signaling / Receptor-ligand complex / Growth factor / Receptor interaction / Activin A / ActRIIa
Function / homology
Function and homology information


inhibin binding / Regulation of signaling by NODAL / activin A complex / inhibin A complex / cardiac fibroblast cell development / inhibin-betaglycan-ActRII complex / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation ...inhibin binding / Regulation of signaling by NODAL / activin A complex / inhibin A complex / cardiac fibroblast cell development / inhibin-betaglycan-ActRII complex / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / activin receptor activity / negative regulation of follicle-stimulating hormone secretion / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / TGFBR3 regulates activin signaling / penile erection / type II activin receptor binding / activin receptor activity, type II / progesterone secretion / Sertoli cell differentiation / striatal medium spiny neuron differentiation / positive regulation of activin receptor signaling pathway / sperm ejaculation / enzyme activator complex / Glycoprotein hormones / negative regulation of macrophage differentiation / negative regulation of phosphorylation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / Sertoli cell proliferation / hemoglobin biosynthetic process / testosterone biosynthetic process / BMP receptor activity / embryonic skeletal system development / activin receptor complex / activin receptor activity, type I / cellular response to follicle-stimulating hormone stimulus / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / cellular response to cholesterol / pattern specification process / activin binding / cellular response to BMP stimulus / 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 / mesodermal cell differentiation / regulation of nitric oxide biosynthetic process / determination of left/right symmetry / anterior/posterior pattern specification / odontogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of transcription by RNA polymerase III / growth factor binding / negative regulation of G1/S transition of mitotic cell cycle / 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 / positive regulation of collagen biosynthetic process / androgen metabolic process / cellular response to angiotensin / positive regulation of SMAD protein signal transduction / hair follicle development / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / hematopoietic progenitor cell differentiation / coreceptor activity / ovarian follicle development / extrinsic apoptotic signaling pathway / positive regulation of erythrocyte differentiation / erythrocyte differentiation / cytokine activity / PDZ domain binding / growth factor activity / defense response / negative regulation of cell growth / hormone activity / cellular response to growth factor stimulus / autophagy / male gonad development / positive regulation of protein phosphorylation / cytokine-mediated signaling pathway / osteoblast differentiation / nervous system development / cell-cell signaling / spermatogenesis / cellular response to hypoxia / transcription by RNA polymerase II / cell differentiation
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. / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Inhibin beta A chain / Activin receptor type-2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsChu, K.Y. / Malik, A. / Thamilselvan, V. / Martinez-Hackert, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121499 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Type II BMP and activin receptors BMPR2 and ACVR2A share a conserved mode of growth factor recognition.
Authors: Chu, K.Y. / Malik, A. / Thamilselvan, V. / Martinez-Hackert, E.
History
DepositionMar 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type-2A
C: Activin receptor type-2A
E: Activin receptor type-2A
G: Activin receptor type-2A
B: Inhibin beta A chain
D: Inhibin beta A chain
F: Inhibin beta A chain
H: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,95616
Polymers107,1868
Non-polymers1,7708
Water724
1
A: Activin receptor type-2A
B: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2394
Polymers26,7962
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Activin receptor type-2A
D: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2394
Polymers26,7962
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Activin receptor type-2A
F: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2394
Polymers26,7962
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Activin receptor type-2A
H: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2394
Polymers26,7962
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.610, 82.540, 151.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 27 through 55 or (resid 56...
21(chain C and (resid 27 through 66 or (resid 67...
31(chain E and (resid 27 through 54 or (resid 55...
41(chain G and (resid 27 through 54 or (resid 55...
12(chain B and (resid 311 or (resid 312 through 313...
22(chain D and (resid 311 or (resid 312 through 313...
32(chain F and (resid 311 or (resid 312 through 313...
42(chain H and ((resid 311 through 313 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRASPASP(chain A and (resid 27 through 55 or (resid 56...AA27 - 5527 - 55
121LYSLYSLYSLYS(chain A and (resid 27 through 55 or (resid 56...AA5656
131THRTHRMETMET(chain A and (resid 27 through 55 or (resid 56...AA27 - 12027 - 120
141THRTHRMETMET(chain A and (resid 27 through 55 or (resid 56...AA27 - 12027 - 120
151THRTHRMETMET(chain A and (resid 27 through 55 or (resid 56...AA27 - 12027 - 120
161THRTHRMETMET(chain A and (resid 27 through 55 or (resid 56...AA27 - 12027 - 120
211THRTHRASNASN(chain C and (resid 27 through 66 or (resid 67...CB27 - 6627 - 66
221ILEILEILEILE(chain C and (resid 27 through 66 or (resid 67...CB6767
231THRTHRMETMET(chain C and (resid 27 through 66 or (resid 67...CB27 - 12027 - 120
241THRTHRMETMET(chain C and (resid 27 through 66 or (resid 67...CB27 - 12027 - 120
251THRTHRMETMET(chain C and (resid 27 through 66 or (resid 67...CB27 - 12027 - 120
261THRTHRMETMET(chain C and (resid 27 through 66 or (resid 67...CB27 - 12027 - 120
311THRTHRLYSLYS(chain E and (resid 27 through 54 or (resid 55...EC27 - 5427 - 54
321ASPASPLYSLYS(chain E and (resid 27 through 54 or (resid 55...EC55 - 5655 - 56
331THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
341THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
351THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
361THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
371THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
381THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
391THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
3101THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
3111THRTHRMETMET(chain E and (resid 27 through 54 or (resid 55...EC27 - 12027 - 120
411THRTHRLYSLYS(chain G and (resid 27 through 54 or (resid 55...GD27 - 5427 - 54
421ASPASPLYSLYS(chain G and (resid 27 through 54 or (resid 55...GD55 - 5655 - 56
431THRTHRMETMET(chain G and (resid 27 through 54 or (resid 55...GD27 - 12027 - 120
441THRTHRMETMET(chain G and (resid 27 through 54 or (resid 55...GD27 - 12027 - 120
451THRTHRMETMET(chain G and (resid 27 through 54 or (resid 55...GD27 - 12027 - 120
461THRTHRMETMET(chain G and (resid 27 through 54 or (resid 55...GD27 - 12027 - 120
112GLYGLYGLYGLY(chain B and (resid 311 or (resid 312 through 313...BE3111
122LEULEUGLUGLU(chain B and (resid 311 or (resid 312 through 313...BE312 - 3132 - 3
132GLYGLYSERSER(chain B and (resid 311 or (resid 312 through 313...BE311 - 4261 - 116
142GLYGLYSERSER(chain B and (resid 311 or (resid 312 through 313...BE311 - 4261 - 116
152GLYGLYSERSER(chain B and (resid 311 or (resid 312 through 313...BE311 - 4261 - 116
162GLYGLYSERSER(chain B and (resid 311 or (resid 312 through 313...BE311 - 4261 - 116
212GLYGLYGLYGLY(chain D and (resid 311 or (resid 312 through 313...DF3111
222LEULEUGLUGLU(chain D and (resid 311 or (resid 312 through 313...DF312 - 3132 - 3
232GLYGLYSERSER(chain D and (resid 311 or (resid 312 through 313...DF311 - 4261 - 116
242GLYGLYSERSER(chain D and (resid 311 or (resid 312 through 313...DF311 - 4261 - 116
252GLYGLYSERSER(chain D and (resid 311 or (resid 312 through 313...DF311 - 4261 - 116
262GLYGLYSERSER(chain D and (resid 311 or (resid 312 through 313...DF311 - 4261 - 116
312GLYGLYGLYGLY(chain F and (resid 311 or (resid 312 through 313...FG3111
322LEULEUGLUGLU(chain F and (resid 311 or (resid 312 through 313...FG312 - 3132 - 3
332GLYGLYSERSER(chain F and (resid 311 or (resid 312 through 313...FG311 - 4261 - 116
342GLYGLYSERSER(chain F and (resid 311 or (resid 312 through 313...FG311 - 4261 - 116
352GLYGLYSERSER(chain F and (resid 311 or (resid 312 through 313...FG311 - 4261 - 116
362GLYGLYSERSER(chain F and (resid 311 or (resid 312 through 313...FG311 - 4261 - 116
412GLYGLYGLUGLU(chain H and ((resid 311 through 313 and (name N...HH311 - 3131 - 3
422GLYGLYSERSER(chain H and ((resid 311 through 313 and (name N...HH311 - 4261 - 116
432GLYGLYSERSER(chain H and ((resid 311 through 313 and (name N...HH311 - 4261 - 116
442GLYGLYSERSER(chain H and ((resid 311 through 313 and (name N...HH311 - 4261 - 116
452GLYGLYSERSER(chain H and ((resid 311 through 313 and (name N...HH311 - 4261 - 116

NCS ensembles :
ID
1
2

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Components

#1: Protein
Activin receptor type-2A / Activin receptor type IIA / ACTR-IIA / ACTRIIA


Mass: 13804.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2A, ACVR2 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P27037, receptor protein serine/threonine kinase
#2: 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) / Gene: INHBA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08476
#3: 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.: 8 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 100mM Sodium Citrate, 17%PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.14→24.69 Å / Num. obs: 17787 / % possible obs: 95.38 % / Redundancy: 4 % / Biso Wilson estimate: 79.23 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 2.949
Reflection shellResolution: 3.14→3.25 Å / Rmerge(I) obs: 0.473 / Num. unique obs: 1631

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S4Y

1s4y


Resolution: 3.14→24.69 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 1769 9.96 %
Rwork0.2173 15994 -
obs0.2232 17763 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.45 Å2 / Biso mean: 81.2387 Å2 / Biso min: 39.11 Å2
Refinement stepCycle: final / Resolution: 3.14→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 112 4 6332
Biso mean--90.03 65.33 -
Num. residues----808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1176X-RAY DIFFRACTION11.735TORSIONAL
12C1176X-RAY DIFFRACTION11.735TORSIONAL
13E1176X-RAY DIFFRACTION11.735TORSIONAL
14G1176X-RAY DIFFRACTION11.735TORSIONAL
21B1202X-RAY DIFFRACTION11.735TORSIONAL
22D1202X-RAY DIFFRACTION11.735TORSIONAL
23F1202X-RAY DIFFRACTION11.735TORSIONAL
24H1202X-RAY DIFFRACTION11.735TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.14-3.230.37481220.2851125124790
3.23-3.320.32031260.26841165129192
3.32-3.430.35491330.26381199133294
3.43-3.550.30561350.2291228136397
3.55-3.690.2881360.22671230136697
3.69-3.860.31231420.22751234137698
3.86-4.060.25641380.21481257139599
4.06-4.320.24021350.18911267140298
4.32-4.650.22561380.18191248138697
4.65-5.110.2581330.17181265139897
5.11-5.840.2521410.21371256139797
5.85-7.330.24821440.23911260140496
7.33-24.690.30171460.22921260140691
Refinement TLS params.Method: refined / Origin x: 10.1814 Å / Origin y: -11.8725 Å / Origin z: -22.06 Å
111213212223313233
T0.5102 Å20.0097 Å2-0.0142 Å2-0.5762 Å2-0.0196 Å2--0.5674 Å2
L-0.2991 °20.1464 °2-0.0023 °2-0.3231 °2-0.0426 °2--0.0943 °2
S-0.0227 Å °0.1169 Å °-0.0186 Å °0.1394 Å °-0.0443 Å °-0.1711 Å °-0.0453 Å °-0.0332 Å °0.0759 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA27 - 120
2X-RAY DIFFRACTION1allA20 - 21
3X-RAY DIFFRACTION1allC27 - 120
4X-RAY DIFFRACTION1allC20 - 21
5X-RAY DIFFRACTION1allE27 - 120
6X-RAY DIFFRACTION1allE20 - 21
7X-RAY DIFFRACTION1allG27 - 120
8X-RAY DIFFRACTION1allG20 - 21
9X-RAY DIFFRACTION1allB311 - 426
10X-RAY DIFFRACTION1allD311 - 426
11X-RAY DIFFRACTION1allF311 - 426
12X-RAY DIFFRACTION1allH311 - 426
13X-RAY DIFFRACTION1allS1 - 4

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