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- PDB-6sf3: Bone morphogenetic protein 10 (BMP10) in complex with extracellul... -

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Basic information

Entry
Database: PDB / ID: 6sf3
TitleBone morphogenetic protein 10 (BMP10) in complex with extracellular domain of activin receptor-like kinase 1 (ALK1) at 2.3 Angstrom
Components
  • Bone morphogenetic protein 10
  • Serine/threonine-protein kinase receptor R3
KeywordsCYTOKINE / BMP10 / ALK1 / complex / signalling / TGFbeta / BMP
Function / homology
Function and homology information


atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / lymphatic endothelial cell differentiation / positive regulation of cell proliferation involved in heart morphogenesis / regulation of endothelial cell proliferation / positive regulation of sarcomere organization / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / blood vessel maturation ...atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / lymphatic endothelial cell differentiation / positive regulation of cell proliferation involved in heart morphogenesis / regulation of endothelial cell proliferation / positive regulation of sarcomere organization / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / blood vessel maturation / venous blood vessel development / ventricular cardiac muscle cell development / positive regulation of cartilage development / transforming growth factor beta receptor activity / telethonin binding / lymphangiogenesis / positive regulation of chondrocyte differentiation / BMP receptor complex / negative regulation of cardiac muscle hypertrophy / BMP receptor activity / retina vasculature development in camera-type eye / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of endothelial cell differentiation / activin receptor activity, type I / transforming growth factor beta receptor activity, type I / endothelial tube morphogenesis / negative regulation of focal adhesion assembly / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / positive regulation of BMP signaling pathway / heart trabecula formation / receptor serine/threonine kinase binding / adult heart development / negative regulation of cell adhesion / transforming growth factor beta binding / dorsal/ventral pattern formation / blood circulation / wound healing, spreading of epidermal cells / Molecules associated with elastic fibres / negative regulation of endothelial cell migration / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / endocardial cushion morphogenesis / sarcomere organization / positive regulation of Notch signaling pathway / positive regulation of cardiac muscle hypertrophy / regulation of DNA replication / SMAD binding / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / regulation of cardiac muscle contraction / blood vessel remodeling / BMP signaling pathway / positive regulation of cardiac muscle cell proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / negative regulation of cell migration / transforming growth factor beta receptor signaling pathway / kidney development / cytokine activity / growth factor activity / negative regulation of cell growth / hormone activity / cellular response to growth factor stimulus / regulation of blood pressure / Z disc / positive regulation of angiogenesis / heart development / angiogenesis / in utero embryonic development / response to hypoxia / cell adhesion / negative regulation of cell population proliferation / phosphorylation / negative regulation of gene expression / protein serine/threonine kinase activity / neuronal cell body / dendrite / regulation of DNA-templated transcription / positive regulation of gene expression / protein kinase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta (TGF-beta) family ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Cystine-knot cytokine / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 10 / Serine/threonine-protein kinase receptor R3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3000067422 Å
AuthorsGuo, J. / Yu, M. / Li, W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
British Heart FoundationPG/12/54/29734 United Kingdom
British Heart FoundationPG/15/39/31519 United Kingdom
British Heart FoundationPG/17/1/32532 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis of ALK1-mediated signalling by BMP9/BMP10 and their prodomain-bound forms.
Authors: Salmon, R.M. / Guo, J. / Wood, J.H. / Tong, Z. / Beech, J.S. / Lawera, A. / Yu, M. / Grainger, D.J. / Reckless, J. / Morrell, N.W. / Li, W.
History
DepositionJul 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase receptor R3
B: Bone morphogenetic protein 10


Theoretical massNumber of molelcules
Total (without water)22,9652
Polymers22,9652
Non-polymers00
Water43224
1
A: Serine/threonine-protein kinase receptor R3
B: Bone morphogenetic protein 10

A: Serine/threonine-protein kinase receptor R3
B: Bone morphogenetic protein 10


Theoretical massNumber of molelcules
Total (without water)45,9314
Polymers45,9314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area7100 Å2
ΔGint-44 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.269, 58.269, 311.435
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Serine/threonine-protein kinase receptor R3 / SKR3 / Activin receptor-like kinase 1 / ALK-1 / TGF-B superfamily receptor type I / TSR-I


Mass: 10788.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVRL1, ACVRLK1, ALK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P37023, receptor protein serine/threonine kinase
#2: Protein Bone morphogenetic protein 10 / / BMP-10


Mass: 12177.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Cell line (production host): HEK-EBNA / Production host: Homo sapiens (human) / References: UniProt: O95393
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.07 M Amino acids (0.014 M DL-Glutamic acids monohydrate; 0.014 M DL-Alanine; 0.014 M Glycine; 0.014 M DL-Lysine monohydrochloride; 0.014 M DL-Serine), 0.07 M Buffer System 3 (0.07 M ...Details: 0.07 M Amino acids (0.014 M DL-Glutamic acids monohydrate; 0.014 M DL-Alanine; 0.014 M Glycine; 0.014 M DL-Lysine monohydrochloride; 0.014 M DL-Serine), 0.07 M Buffer System 3 (0.07 M Tris(base)/BICINE), 35% Precipitant Mix 4 (9% v/v MPD, 9% w/v PEG 1000, 9% w/ PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→311.44 Å / Num. obs: 15103 / % possible obs: 99.9 % / Redundancy: 14.7 % / Biso Wilson estimate: 46.5309023868 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.075 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1408 / CC1/2: 0.635 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SF1

6sf1


Resolution: 2.3000067422→51.9058333333 Å / SU ML: 0.358600350348 / Cross valid method: THROUGHOUT / σ(F): 1.33792944578 / Phase error: 27.5151156747
RfactorNum. reflection% reflection
Rfree0.243250254795 1292 4.92396813903 %
Rwork0.21397641611 --
obs0.215492606269 14963 99.7832369942 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.9737321218 Å2
Refinement stepCycle: LAST / Resolution: 2.3000067422→51.9058333333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 0 24 1443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006851464786331497
X-RAY DIFFRACTIONf_angle_d0.8495692359062043
X-RAY DIFFRACTIONf_chiral_restr0.050588862781218
X-RAY DIFFRACTIONf_plane_restr0.00593486275068261
X-RAY DIFFRACTIONf_dihedral_angle_d11.810858825920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.39210.3493313089671310.328884343772758X-RAY DIFFRACTION99.4492254733
2.3921-2.5010.3701882600351370.2874976868892774X-RAY DIFFRACTION99.4533652204
2.501-2.63280.269805138011480.2493915584842777X-RAY DIFFRACTION99.7952917093
2.6328-2.79780.35880841451490.2472615853682770X-RAY DIFFRACTION99.6926229508
2.7978-3.01380.3141225893521320.2380578744442768X-RAY DIFFRACTION99.9310820124
3.0138-3.3170.1920631470941500.2145997177652760X-RAY DIFFRACTION99.9313186813
3.317-3.79680.2387196580561170.2030924722432810X-RAY DIFFRACTION99.9658469945
3.7968-4.78310.2045641147311530.1673107637052779X-RAY DIFFRACTION99.9318336742
4.7831-510.2307175428741750.2131336943262751X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.4160126815 Å / Origin y: -17.6787951068 Å / Origin z: -35.6142750508 Å
111213212223313233
T0.459765324487 Å2-0.00325099411558 Å20.0380789994361 Å2-0.376544594312 Å2-0.0406849020107 Å2--0.370216899179 Å2
L0.735050848082 °2-1.98633319022 °2-1.87129023389 °2-2.51478031143 °23.9986797555 °2--5.73890154282 °2
S0.276245336989 Å °0.267649826849 Å °-0.00379702400805 Å °-0.211905068508 Å °-0.334487876295 Å °-0.0201199064171 Å °-0.512056185188 Å °-0.362844817164 Å °0.0517136088534 Å °
Refinement TLS groupSelection details: all

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