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

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Basic information

Entry
Database: PDB / ID: 5oxg
TitleCrystal structure of the ACVR1 (ALK2) kinase in complex with LDN-212854
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 / BMP receptor activity / endocardial cushion fusion / atrial septum primum morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity ...endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / BMP receptor activity / endocardial cushion fusion / atrial septum primum morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / smooth muscle cell differentiation / activin receptor complex / activin receptor activity, type I / endocardial cushion formation / pharyngeal system development / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of 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 / atrioventricular valve morphogenesis / neural crest cell migration / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / SMAD binding / germ cell development / peptide hormone binding / mesoderm formation / positive regulation of intracellular signal transduction / positive regulation of SMAD protein signal transduction / regulation of ossification / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / negative regulation of signal transduction / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / apical part of cell / osteoblast differentiation / 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
Chem-B4B / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsWilliams, E.P. / Sorrell, F.J. / Kopec, J. / Nowak, R.P. / Kupinska, K. / von Delft, F. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Williams, E.P. / Sorrell, F.J. / Kopec, J. / Nowak, R.P. / Kupinska, K. / von Delft, F. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: Bone / Year: 2018
Title: Structural basis for the potent and selective binding of LDN-212854 to the BMP receptor kinase ALK2.
Authors: Williams, E. / Bullock, A.N.
History
DepositionSep 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.5Oct 23, 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)140,07915
Polymers138,1514
Non-polymers1,92811
Water6,359353
1
A: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0244
Polymers34,5381
Non-polymers4873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9843
Polymers34,5381
Non-polymers4472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0244
Polymers34,5381
Non-polymers4873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0464
Polymers34,5381
Non-polymers5093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.860, 102.201, 177.300
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRILEILEAA203 - 4985 - 300
21THRTHRILEILEBB203 - 4985 - 300
12THRTHRLYSLYSAA203 - 4975 - 299
22THRTHRLYSLYSCC203 - 4975 - 299
13VALVALLYSLYSAA204 - 4976 - 299
23VALVALLYSLYSDD204 - 4976 - 299
14THRTHRLYSLYSBB203 - 4975 - 299
24THRTHRLYSLYSCC203 - 4975 - 299
15VALVALILEILEBB204 - 4986 - 300
25VALVALILEILEDD204 - 4986 - 300
16VALVALILEILECC204 - 4986 - 300
26VALVALILEILEDD204 - 4986 - 300

NCS ensembles :
ID
1
2
3
4
5
6

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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
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-B4B / 5-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline


Mass: 406.482 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H22N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG8000 -- 0.2M calcium acetate -- 0.1M cacodylate pH 6.5

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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: Dec 6, 2013
Details: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focusing
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.13→65.65 Å / Num. obs: 88737 / % possible obs: 99.56 % / Observed criterion σ(F): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.052 / Rrim(I) all: 0.093 / Net I/av σ(I): 8.12 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4518 / CC1/2: 0.8 / Rpim(I) all: 0.358 / Rrim(I) all: 0.65 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLM7.2.1data reduction
Aimless7.0.044data scaling
PHASER7.0.044phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9R

3h9r


Resolution: 2.13→65.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.988 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2061 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.17 / SU Rfree Cruickshank DPI: 0.1697 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23243 4290 4.8 %RANDOM
Rwork0.20611 ---
obs0.20736 84441 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.974 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å2-0 Å22.81 Å2
2--1 Å20 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 2.13→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9312 0 134 353 9799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199725
X-RAY DIFFRACTIONr_bond_other_d0.0020.028879
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.96213238
X-RAY DIFFRACTIONr_angle_other_deg0.929320522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08851193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36323.872421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.648151628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3851560
X-RAY DIFFRACTIONr_chiral_restr0.0810.21483
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022025
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7114.654742
X-RAY DIFFRACTIONr_mcbond_other2.7114.654741
X-RAY DIFFRACTIONr_mcangle_it4.1746.9655921
X-RAY DIFFRACTIONr_mcangle_other4.1736.9655922
X-RAY DIFFRACTIONr_scbond_it2.9324.844981
X-RAY DIFFRACTIONr_scbond_other2.9314.844981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5337.1667308
X-RAY DIFFRACTIONr_long_range_B_refined11.35154.05911153
X-RAY DIFFRACTIONr_long_range_B_other11.35254.03511151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A190420.06
12B190420.06
21A191540.06
22C191540.06
31A189820.06
32D189820.06
41B191140.05
42C191140.05
51B188020.06
52D188020.06
61C191020.05
62D191020.05
LS refinement shellResolution: 2.13→2.155 Å
RfactorNum. reflection% reflection
Rfree0.319 335 5 %
Rwork0.311 6181 -
obs--99.54 %

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