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- PDB-6sf2: Ternary complex of human bone morphogenetic protein 9 (BMP9) grow... -

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Basic information

Entry
Database: PDB / ID: 6sf2
TitleTernary complex of human bone morphogenetic protein 9 (BMP9) growth factor domain, its prodomain and extracellular domain of activin receptor-like kinase 1 (ALK1).
Components
  • (Growth/differentiation factor 2) x 2
  • Serine/threonine-protein kinase receptor R3
KeywordsCYTOKINE / BMP9 / ALK1 / prodomain / ternary complex / signalling / TGFbeta / BMP
Function / homology
Function and homology information


lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / blood vessel maturation / venous blood vessel development / positive regulation of cartilage development / transforming growth factor beta receptor activity / lymphangiogenesis ...lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / blood vessel maturation / venous blood vessel development / positive regulation of cartilage development / 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 / 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 / negative regulation of focal adhesion assembly / endothelial tube morphogenesis / 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 / negative regulation of cell adhesion / transforming growth factor beta binding / dorsal/ventral pattern formation / blood circulation / cartilage development / wound healing, spreading of epidermal cells / blood vessel morphogenesis / negative regulation of endothelial cell migration / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / negative regulation of DNA replication / 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 / blood vessel remodeling / vasculogenesis / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / protein serine/threonine kinase activator activity / negative regulation of angiogenesis / negative regulation of cell migration / ossification / transforming growth factor beta receptor signaling pathway / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / negative regulation of cell growth / cellular response to growth factor stimulus / regulation of blood pressure / osteoblast differentiation / positive regulation of angiogenesis / heart development / angiogenesis / intracellular iron ion homeostasis / in utero embryonic development / transcription by RNA polymerase II / response to hypoxia / 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 / protein kinase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane
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
Serine/threonine-protein kinase receptor R3 / Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 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.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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: Growth/differentiation factor 2
C: Growth/differentiation factor 2
D: Serine/threonine-protein kinase receptor R3
E: Growth/differentiation factor 2
F: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4348
Polymers111,9926
Non-polymers4422
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-66 kcal/mol
Surface area30310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.610, 72.610, 438.485
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROLEULEU(chain 'A' and (resid 30 through 60 or (resid 61...AA30 - 10310 - 83
221PROPROLEULEU(chain 'D' and (resid 30 through 36 or (resid 37...DD30 - 10310 - 83
132SERSERLYSLYS(chain 'B' and (resid 325 through 336 or (resid 337...BB325 - 3906 - 71
142CYSCYSARGARG(chain 'B' and (resid 325 through 336 or (resid 337...BB393 - 42974 - 110
252SERSERLYSLYS(chain 'E' and ((resid 325 and (name N or name...EE325 - 3906 - 71
262CYSCYSARGARG(chain 'E' and ((resid 325 and (name N or name...EE393 - 42974 - 110

NCS ensembles :
ID
1
2

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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.: 2
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 Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12102.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Cell line (production host): HEK-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q9UK05
#3: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 33104.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Cell line (production host): HEK-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q9UK05
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.14 M potassium sodium tartrate, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 3.3→62.88 Å / Num. obs: 19622 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 90.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.052 / Rrim(I) all: 0.163 / Net I/σ(I): 13.3
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2834 / CC1/2: 0.779 / Rpim(I) all: 0.369 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FAO, 4YCG

4fao

4ycg


Resolution: 3.3→62.25 Å / SU ML: 0.4924 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.5581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2743 996 5.1 %
Rwork0.2426 18522 -
obs0.2441 19518 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.58 Å2
Refinement stepCycle: LAST / Resolution: 3.3→62.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 28 9 4384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184488
X-RAY DIFFRACTIONf_angle_d0.48966136
X-RAY DIFFRACTIONf_chiral_restr0.0422718
X-RAY DIFFRACTIONf_plane_restr0.0033787
X-RAY DIFFRACTIONf_dihedral_angle_d10.9589634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.470.34471500.30752625X-RAY DIFFRACTION99.93
3.47-3.690.32781460.28332635X-RAY DIFFRACTION99.89
3.69-3.980.2881500.26772623X-RAY DIFFRACTION99.96
3.98-4.380.25411330.22312657X-RAY DIFFRACTION99.96
4.38-5.010.21771480.20092642X-RAY DIFFRACTION100
5.01-6.310.28371290.24492665X-RAY DIFFRACTION100
6.31-62.250.28181400.24282675X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -23.2435955183 Å / Origin y: -20.3457557922 Å / Origin z: -11.4726290322 Å
111213212223313233
T0.58194569458 Å20.150402090821 Å20.0603266094604 Å2-0.621233885191 Å20.0940461379944 Å2--0.746879143477 Å2
L0.433867473125 °20.07605747223 °2-0.538980349733 °2-0.801855628732 °20.390745145245 °2--1.18416219097 °2
S0.0376298875668 Å °-0.116324086007 Å °-0.0289120473988 Å °0.0191895145558 Å °0.0851551448839 Å °0.09561784345 Å °-0.0342887723743 Å °0.0481441147905 Å °-0.122735566358 Å °
Refinement TLS groupSelection details: all

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