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- PDB-5oy6: Crystal structure of the ACVR1 (ALK2) kinase in complex with cycl... -

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Basic information

Entry
Database: PDB / ID: 5oy6
TitleCrystal structure of the ACVR1 (ALK2) kinase in complex with cyclical inhibitor OD36.
ComponentsActivin receptor type-1
KeywordsSIGNALING PROTEIN / Kinase / ALK2 / Receptor / BMP / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / atrial septum primum morphogenesis / endocardial cushion fusion / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity / smooth muscle cell differentiation ...endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / atrial septum primum morphogenesis / endocardial cushion fusion / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity / smooth muscle cell differentiation / activin receptor complex / endocardial cushion formation / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / pharyngeal system development / transforming growth factor beta receptor activity, type III / activin binding / cellular response to BMP stimulus / negative regulation of activin receptor signaling pathway / activin receptor signaling pathway / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / transforming growth factor beta binding / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / SMAD binding / germ cell development / positive regulation of intracellular signal transduction / peptide hormone binding / mesoderm formation / positive regulation of SMAD protein signal transduction / regulation of ossification / BMP signaling pathway / positive regulation of bone mineralization / negative regulation of signal transduction / positive regulation of osteoblast differentiation / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / osteoblast differentiation / apical part of cell / heart development / in utero embryonic development / cell differentiation / protein kinase activity / positive regulation of cell migration / cadherin binding / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cyclical inhibitor OD36 / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsWilliams, E.P. / Pinkas, D.M. / Krojer, T. / Kupinska, K. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: Establishment and characterization of endothelial colony forming cells as a surrogate model for Fibrodysplasia Ossificans Progressiva
Authors: Sanchez-Duffhues, G. / Orlova, V. / Benderitter, P. / Williams, E.P. / Garcia de Vinuesa, A. / Caradec, J. / van Wijhe, M. / de Boer, H. / Goumans, M.J. / Eeckhoff, M. / Morales Piga, A. / ...Authors: Sanchez-Duffhues, G. / Orlova, V. / Benderitter, P. / Williams, E.P. / Garcia de Vinuesa, A. / Caradec, J. / van Wijhe, M. / de Boer, H. / Goumans, M.J. / Eeckhoff, M. / Morales Piga, A. / Bachiller, J. / Koolwijk, P. / Bullock, A. / Hoflack, J. / ten Dijke, P.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type-1
B: Activin receptor type-1
C: Activin receptor type-1
D: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,59810
Polymers138,1514
Non-polymers1,4476
Water1,26170
1
A: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9934
Polymers34,5381
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8682
Polymers34,5381
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8682
Polymers34,5381
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8682
Polymers34,5381
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.260, 103.530, 84.840
Angle α, β, γ (deg.)90.00, 116.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Activin receptor type-1 / Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine- ...Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine-protein kinase receptor R1 / SKR1 / TGF-B superfamily receptor type I / TSR-I


Mass: 34537.633 Da / Num. of mol.: 4 / Mutation: Q207D
Source method: isolated from a genetically manipulated source
Details: Contains a Q207D mutation compared to the wt gene - Q04771
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9
References: UniProt: Q04771, receptor protein serine/threonine kinase
#2: Chemical
ChemComp-B4E / cyclical inhibitor OD36


Mass: 330.769 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H15ClN4O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.3M magnesium formate, 0.1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2014 / Details: Compound Refractive Lenses
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.56→75.39 Å / Num. obs: 42050 / % possible obs: 99.91 % / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 63.101 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.076 / Net I/σ(I): 8.7
Reflection shellResolution: 2.56→2.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4176 / CC1/2: 0.904 / Rrim(I) all: 0.578 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLM7.2.1data reduction
Aimless7.0.044data scaling
PHASER7.0.044phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9R

3h9r


Resolution: 2.56→71.903 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2123 5.06 %Random selection
Rwork0.2111 ---
obs0.2129 41945 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→71.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8873 0 100 70 9043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069181
X-RAY DIFFRACTIONf_angle_d0.80312519
X-RAY DIFFRACTIONf_dihedral_angle_d13.4915401
X-RAY DIFFRACTIONf_chiral_restr0.0511431
X-RAY DIFFRACTIONf_plane_restr0.0051572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.61960.38171580.30542628X-RAY DIFFRACTION99
2.6196-2.68510.3111170.30822619X-RAY DIFFRACTION99
2.6851-2.75770.29841330.29372642X-RAY DIFFRACTION99
2.7577-2.83880.33481230.28272675X-RAY DIFFRACTION100
2.8388-2.93050.31461340.27552645X-RAY DIFFRACTION99
2.9305-3.03520.30311160.25592686X-RAY DIFFRACTION100
3.0352-3.15670.29871370.24882653X-RAY DIFFRACTION100
3.1567-3.30040.31891340.24552626X-RAY DIFFRACTION100
3.3004-3.47440.2991640.24872642X-RAY DIFFRACTION100
3.4744-3.69210.26531220.21752712X-RAY DIFFRACTION100
3.6921-3.97710.2271440.20012640X-RAY DIFFRACTION100
3.9771-4.37730.23041310.17752659X-RAY DIFFRACTION100
4.3773-5.01060.1871750.17152644X-RAY DIFFRACTION100
5.0106-6.31220.21391860.20042644X-RAY DIFFRACTION100
6.3122-71.93140.22991490.18472707X-RAY DIFFRACTION99
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)
15.35560.16383.05686.99123.45984.08430.02230.1237-0.26830.65730.7538-0.67540.48831.2812-0.73170.54390.08820.07050.59-0.06330.514922.6826-9.4934-21.2045
24.2241-2.9224-3.50854.65542.17578.7826-0.0965-0.61120.3709-0.04570.4095-0.26280.1040.2631-0.30780.4084-0.0504-0.05530.39490.04030.451416.0834-2.4397-20.3701
34.94970.46441.28772.68350.31175.482-0.1567-0.19540.2040.08970.27550.32050.1103-1.0285-0.13910.41740.06690.03640.49180.13160.3716-1.7868-2.7206-22.9829
47.484-1.1418-0.37945.0034-2.16987.39830.23-0.07910.2668-0.44760.15560.19870.1576-0.4781-0.36110.5103-0.08710.01140.45410.06240.39074.522338.5969-33.8684
53.4353-0.2388-1.51392.25370.22035.25250.0552-0.999-0.15950.21480.18350.03940.03840.376-0.22490.4829-0.0311-0.02270.95020.20980.487613.408435.1803-13.8881
63.40280.85710.48646.3427-0.06975.16550.48930.0354-0.70030.71680.20640.06110.72680.9406-0.55220.83640.20380.01281.47120.37740.714816.307125.1788-5.986
76.2925-0.79863.0149.168-2.83685.7940.36890.39030.2238-1.3696-0.92390.8138-0.4959-0.56560.32370.91260.3427-0.21090.9679-0.24640.817-28.59122.5573-67.6421
82.18031.83260.92649.26133.14141.47070.8313-0.1478-0.1025-1.1733-1.50280.9866-0.0236-0.74370.62050.80150.1847-0.18851.1095-0.10520.8288-27.81722.9601-60.7809
93.7992-0.25050.9917.04281.57132.26830.7442-0.5133-0.1443-0.0434-1.0628-0.4690.0802-0.34650.29480.5196-0.0384-0.01230.74710.18780.461-14.567214.5261-50.5021
107.6053-4.4875-3.47743.74651.22593.85560.36610.83560.15710.0256-0.6289-2.0814-0.1244-0.78360.40150.87870.11780.05081.41160.08361.3222-14.38427.3312-6.1809
113.20492.00290.30334.6842-0.85222.81610.1682-0.0477-0.23510.0086-0.5481-0.7432-0.10080.13640.34820.43910.0363-0.06170.70540.03310.7859-32.11722.5091-11.6682
121.24710.5386-1.00523.2013-0.47821.73560.24310.0319-0.0851-0.1148-0.39330.180.3504-0.60570.13560.7336-0.1527-0.08071.0223-0.14021.09-45.83079.2462-12.43
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 204 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 307 )
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 498 )
4X-RAY DIFFRACTION4chain 'B' and (resid 204 through 289 )
5X-RAY DIFFRACTION5chain 'B' and (resid 290 through 460 )
6X-RAY DIFFRACTION6chain 'B' and (resid 461 through 498 )
7X-RAY DIFFRACTION7chain 'C' and (resid 204 through 249 )
8X-RAY DIFFRACTION8chain 'C' and (resid 250 through 295 )
9X-RAY DIFFRACTION9chain 'C' and (resid 296 through 498 )
10X-RAY DIFFRACTION10chain 'D' and (resid 204 through 220 )
11X-RAY DIFFRACTION11chain 'D' and (resid 221 through 453 )
12X-RAY DIFFRACTION12chain 'D' and (resid 454 through 495 )

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