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- PDB-6sf1: Bone morphogenetic protein 10 (BMP10) complexed with extracellula... -

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Basic information

Entry
Database: PDB / ID: 6sf1
TitleBone morphogenetic protein 10 (BMP10) complexed with extracellular domain of activin receptor-like kinase 1 (ALK1).
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 / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / positive regulation of cell proliferation involved in heart morphogenesis / dorsal aorta morphogenesis / positive regulation of sarcomere organization / blood vessel maturation / positive regulation of epithelial cell differentiation ...atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / positive regulation of cell proliferation involved in heart morphogenesis / dorsal aorta morphogenesis / positive regulation of sarcomere organization / blood vessel maturation / positive regulation of epithelial cell differentiation / venous blood vessel development / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / transforming growth factor beta receptor activity / lymphangiogenesis / positive regulation of chondrocyte differentiation / BMP receptor complex / retina vasculature development in camera-type eye / BMP receptor activity / negative regulation of cardiac muscle hypertrophy / 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 / activin binding / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of BMP signaling pathway / receptor serine/threonine kinase binding / adult heart development / heart trabecula formation / negative regulation of cell adhesion / transforming growth factor beta binding / dorsal/ventral pattern formation / blood circulation / wound healing, spreading of epidermal cells / negative regulation of endothelial cell migration / Molecules associated with elastic fibres / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / sarcomere organization / positive regulation of Notch signaling pathway / positive regulation of cardiac muscle hypertrophy / negative regulation of endothelial cell proliferation / regulation of DNA replication / SMAD binding / 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 / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / 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 / 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. / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta-related / 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 / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
NICKEL (II) ION / Bone morphogenetic protein 10 / Activin receptor type-1-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSalmon, R.M. / Guo, 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 30, 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.page_first / _citation.page_last ..._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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,2597
Polymers22,9652
Non-polymers2935
Water905
1
A: Serine/threonine-protein kinase receptor R3
B: Bone morphogenetic protein 10
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)46,51814
Polymers45,9314
Non-polymers58710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area8720 Å2
ΔGint-142 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.570, 57.570, 304.062
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)

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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: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.57 Å3/Da / Density % sol: 65.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 17% PEG 3350, 0.175 M NH4I, 0.1 M HEPES pH 7.8

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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: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→25.03 Å / Num. obs: 8187 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 66.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.052 / Rsym value: 0.097 / Net I/σ(I): 9.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1151 / CC1/2: 0.862 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FAO

4fao


Resolution: 2.8→24.93 Å / SU ML: 0.3982 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 788 9.72 %
Rwork0.2441 7320 -
obs0.2477 8108 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.37 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 5 5 1429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171457
X-RAY DIFFRACTIONf_angle_d0.48781977
X-RAY DIFFRACTIONf_chiral_restr0.0416214
X-RAY DIFFRACTIONf_plane_restr0.0036253
X-RAY DIFFRACTIONf_dihedral_angle_d13.1136538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.970.36271300.30681172X-RAY DIFFRACTION99.92
2.98-3.20.29721180.27571204X-RAY DIFFRACTION99.55
3.2-3.530.30021320.24681159X-RAY DIFFRACTION99.54
3.53-4.030.27011280.21761203X-RAY DIFFRACTION99.4
4.04-5.080.23731160.21081255X-RAY DIFFRACTION99.64
5.08-24.930.28351640.26821327X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: 20.7810866251 Å / Origin y: -17.7877611907 Å / Origin z: -34.8113700928 Å
111213212223313233
T0.463764857507 Å20.102838130931 Å20.0377862671392 Å2-0.484272061283 Å2-0.0167512808471 Å2--0.470602871363 Å2
L1.79641354601 °2-2.05725975198 °2-2.3679554308 °2-3.50493527795 °24.61780898805 °2--8.38238680898 °2
S0.354128726748 Å °0.550140473527 Å °-0.0427237350181 Å °-0.397430076285 Å °-0.472351984051 Å °0.0020199579713 Å °-0.56243045005 Å °-0.610816881381 Å °0.123447435521 Å °
Refinement TLS groupSelection details: all

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