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- PDB-6uns: Kinase domain of ALK2-K492A/K493A with LDN-193189 -

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Basic information

Entry
Database: PDB / ID: 6uns
TitleKinase domain of ALK2-K492A/K493A with LDN-193189
ComponentsActivin receptor type-1
KeywordsTRANSFERASE / Kinase
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-LDN / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAgnew, C. / Jura, N.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization.
Authors: Agnew, C. / Ayaz, P. / Kashima, R. / Loving, H.S. / Ghatpande, P. / Kung, J.E. / Underbakke, E.S. / Shan, Y. / Shaw, D.E. / Hata, A. / Jura, N.
History
DepositionOct 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 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

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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)76,9324
Polymers76,1192
Non-polymers8132
Water18010
1
A: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4662
Polymers38,0591
Non-polymers4061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4662
Polymers38,0591
Non-polymers4061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.000, 83.641, 137.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER(chain 'A' and (resid 204 through 296 or (resid 297...AA204 - 27235 - 103
12SERSERILEILE(chain 'A' and (resid 204 through 296 or (resid 297...AA276 - 312107 - 143
13GLYGLYILEILE(chain 'A' and (resid 204 through 296 or (resid 297...AA315 - 323146 - 154
14LYSLYSASPASP(chain 'A' and (resid 204 through 296 or (resid 297...AA329 - 336160 - 167
15LYSLYSASPASP(chain 'A' and (resid 204 through 296 or (resid 297...AA338 - 394169 - 225
16PHEPHETHRTHR(chain 'A' and (resid 204 through 296 or (resid 297...AA396 - 496227 - 327
17LDNLDNLDNLDN(chain 'A' and (resid 204 through 296 or (resid 297...AC501
21VALVALSERSER(chain 'B' and (resid 204 through 229 or (resid 230...BB204 - 27235 - 103
22SERSERSERSER(chain 'B' and (resid 204 through 229 or (resid 230...BB275106
23THRTHRILEILE(chain 'B' and (resid 204 through 229 or (resid 230...BB277 - 312108 - 143
24GLYGLYILEILE(chain 'B' and (resid 204 through 229 or (resid 230...BB315 - 323146 - 154
25LYSLYSASPASP(chain 'B' and (resid 204 through 229 or (resid 230...BB329 - 336160 - 167
26LYSLYSASPASP(chain 'B' and (resid 204 through 229 or (resid 230...BB338 - 394169 - 225
27PHEPHETHRTHR(chain 'B' and (resid 204 through 229 or (resid 230...BB396 - 496227 - 327
28LDNLDNLDNLDN(chain 'B' and (resid 204 through 229 or (resid 230...BD501

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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: 38059.336 Da / Num. of mol.: 2 / Fragment: Kinase domain / Mutation: K492A, K493A
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
#2: Chemical ChemComp-LDN / 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline


Mass: 406.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05 M PIPES pH 7, 0.01 M DTT, 10 %w/v PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 2.3→48.75 Å / Num. obs: 31655 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 34.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.12 / Rrim(I) all: 0.314 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.343 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3042 / CC1/2: 0.632 / Rpim(I) all: 0.942 / Rrim(I) all: 2.527 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q4U

3q4u


Resolution: 2.3→48.75 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.239
RfactorNum. reflection% reflection
Rfree0.2618 1625 5.14 %
Rwork0.2123 --
obs0.2148 31600 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4511 0 62 10 4583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774696
X-RAY DIFFRACTIONf_angle_d0.99946401
X-RAY DIFFRACTIONf_chiral_restr0.0574722
X-RAY DIFFRACTIONf_plane_restr0.006805
X-RAY DIFFRACTIONf_dihedral_angle_d23.43661662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.29611340.27152449X-RAY DIFFRACTION99.96
2.37-2.440.32071460.25592443X-RAY DIFFRACTION99.88
2.44-2.530.31841480.25062437X-RAY DIFFRACTION99.96
2.53-2.630.26131280.23552471X-RAY DIFFRACTION100
2.63-2.750.2821370.22212460X-RAY DIFFRACTION99.96
2.75-2.90.27551350.21522471X-RAY DIFFRACTION99.96
2.9-3.080.33621290.22042487X-RAY DIFFRACTION99.92
3.08-3.320.2761240.2212512X-RAY DIFFRACTION99.96
3.32-3.650.28241300.20582503X-RAY DIFFRACTION99.96
3.65-4.180.24031250.20362522X-RAY DIFFRACTION99.85
4.18-5.260.20751340.18692548X-RAY DIFFRACTION100
5.26-48.750.24171550.19982672X-RAY DIFFRACTION99.86

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