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- PDB-5s8a: XChem group deposition -- Crystal Structure of human ACVR1 in com... -

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Basic information

Entry
Database: PDB / ID: 5s8a
TitleXChem group deposition -- Crystal Structure of human ACVR1 in complex with NU074484b
ComponentsActivin receptor type-1
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / 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
Similarity search - Domain/homology
Chem-LU8 / L(+)-TARTARIC ACID / (4S)-imidazolidine-4-carbonitrile / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.3 Å
AuthorsWilliams, E.P. / Adamson, R.J. / Smil, D. / Krojer, T. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: XChem group deposition
Authors: Williams, E.P. / Adamson, R.J. / Smil, D. / Krojer, T. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Bullock, A.N.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-1
B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,68930
Polymers69,0752
Non-polymers3,61428
Water14,844824
1
A: Activin receptor type-1
hetero molecules

B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,68930
Polymers69,0752
Non-polymers3,61428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6420 Å2
ΔGint-50 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.217, 84.858, 88.090
Angle α, β, γ (deg.)90.000, 130.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q04771, receptor protein serine/threonine kinase

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Non-polymers , 7 types, 852 molecules

#2: Chemical
ChemComp-LU8 / 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine


Mass: 432.555 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H32N2O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-XKY / (4S)-imidazolidine-4-carbonitrile


Mass: 97.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7N3
#7: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.6 Å3/Da / Density % sol: 52.67 % / Mosaicity: 0.06 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.3→66.52 Å / Num. obs: 126180 / % possible obs: 73.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Net I/σ(I): 14 / Num. measured all: 769831 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.372.21.573759333980.421.1611.9710.413.6
4.12-66.526.90.0263864256020.9990.0110.02859.499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6SRH

6srh


Resolution: 1.3→48.07 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.078 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 6324 5 %RANDOM
Rwork0.1566 ---
obs0.1577 119856 73.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.66 Å2 / Biso mean: 17.892 Å2 / Biso min: 9.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.47 Å2
2---0.44 Å20 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 1.3→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 274 825 5662
Biso mean--28.57 33.73 -
Num. residues----575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174850
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.697017
X-RAY DIFFRACTIONr_angle_other_deg1.5151.62811137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06921.807249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22515843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0861533
X-RAY DIFFRACTIONr_chiral_restr0.0990.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025735
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021194
X-RAY DIFFRACTIONr_mcbond_it1.6641.6052409
X-RAY DIFFRACTIONr_mcbond_other1.6631.6052408
X-RAY DIFFRACTIONr_mcangle_it2.4712.3983041
LS refinement shellResolution: 1.304→1.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 36 -
Rwork0.395 846 -
all-882 -
obs--6.96 %

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