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- PDB-5i05: Crystal structure of human BMP9 at 1.87 A resolution -

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Basic information

Entry
Database: PDB / ID: 5i05
TitleCrystal structure of human BMP9 at 1.87 A resolution
ComponentsGrowth/differentiation factor 2
KeywordsSIGNALING PROTEIN / GROWTH DIFFERENTIATION FACTOR 2 / CELL PROLIFERATION SIGNAL / CYTOKINE / ANGIOGENESIS
Function / homology
Function and homology information


positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of bicellular tight junction assembly / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis ...positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of bicellular tight junction assembly / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / negative regulation of DNA replication / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / BMP signaling pathway / vasculogenesis / positive regulation of endothelial cell proliferation / ossification / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / negative regulation of cell growth / positive regulation of angiogenesis / osteoblast differentiation / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / 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. / Cystine-knot cytokine
Similarity search - Domain/homology
Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSaito, T. / Bokhove, M. / Jovine, L.
Funding support Sweden, 7items
OrganizationGrant numberCountry
Karolinska Institutet Sweden
Center for Biosciences Sweden
Swedish Research Council2012-5093 Sweden
Gustafsson Foundation for Research in Natural Sciences and Medicine Sweden
Sven and Ebba-Christina Hagberg foundation Sweden
European Molecular Biology Organization
European UnionERC 260759
Citation
Journal: Cell Rep / Year: 2017
Title: Structural Basis of the Human Endoglin-BMP9 Interaction: Insights into BMP Signaling and HHT1.
Authors: Saito, T. / Bokhove, M. / Croci, R. / Zamora-Caballero, S. / Han, L. / Letarte, M. / de Sanctis, D. / Jovine, L.
#1: Journal: J. Biol. Chem. / Year: 2005
Title: Crystal structure of BMP-9 and functional interactions with pro-region and receptors.
Authors: Brown, M.A. / Zhao, Q. / Baker, K.A. / Naik, C. / Chen, C. / Pukac, L. / Singh, M. / Tsareva, T. / Parice, Y. / Mahoney, A. / Roschke, V. / Sanyal, I. / Choe, S.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Structure of bone morphogenetic protein 9 procomplex.
Authors: Mi, L.Z. / Brown, C.T. / Gao, Y. / Tian, Y. / Le, V.Q. / Walz, T. / Springer, T.A.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.page_last ..._citation.country / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2873
Polymers12,1031
Non-polymers1842
Water93752
1
A: Growth/differentiation factor 2
hetero molecules

A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5746
Polymers24,2062
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
Buried area3360 Å2
ΔGint-26 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.060, 71.060, 145.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-1047-

HOH

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Components

#1: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12102.971 Da / Num. of mol.: 1 / Fragment: UNP residues 320-429
Source method: isolated from a genetically manipulated source
Details: Mature BMP9 / Source: (gene. exp.) Homo sapiens (human) / Cell: Endothelial / Gene: GDF2, BMP9 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9UK05
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.81 Å3/Da / Density % sol: 67.77 % / Description: Rectangular Prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 1.0 M LiCl, 4% (v/v) PEG6000, 0.1 M NA-CITRATE / PH range: 3.0-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2014
RadiationMonochromator: Si Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.87→41.36 Å / Num. obs: 15763 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.95
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.39 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDS(November 3, 2014)data reduction
XSCALE(November 3, 2014 BUILT=20141103)data scaling
PHASER(2.56)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZK

1kzk


Resolution: 1.87→41.36 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1576 10 %Random selection
Rwork0.2135 ---
obs0.2155 15756 99.4 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms831 0 12 52 895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005874
X-RAY DIFFRACTIONf_angle_d0.7341186
X-RAY DIFFRACTIONf_dihedral_angle_d14.726326
X-RAY DIFFRACTIONf_chiral_restr0.047128
X-RAY DIFFRACTIONf_plane_restr0.005148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8701-1.93050.36331390.35721257X-RAY DIFFRACTION100
1.9305-1.99950.33491410.33431263X-RAY DIFFRACTION100
1.9995-2.07950.32011430.28881264X-RAY DIFFRACTION100
2.0795-2.17420.29591410.25391279X-RAY DIFFRACTION100
2.1742-2.28880.29571420.23821282X-RAY DIFFRACTION100
2.2888-2.43220.20721410.21651269X-RAY DIFFRACTION99
2.4322-2.61990.26551440.21261287X-RAY DIFFRACTION100
2.6199-2.88350.23171430.20921280X-RAY DIFFRACTION100
2.8835-3.30060.19291440.20761304X-RAY DIFFRACTION99
3.3006-4.15780.19821470.19131320X-RAY DIFFRACTION99
4.1578-41.36980.22561510.19081375X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -10.6333 Å / Origin y: -10.984 Å / Origin z: -23.2336 Å
111213212223313233
T0.33 Å2-0.0651 Å2-0.0389 Å2-0.2932 Å2-0.0134 Å2--0.3098 Å2
L3.2836 °20.9207 °2-1.2534 °2-0.8659 °20.0352 °2--1.4834 °2
S-0.3516 Å °-0.0036 Å °0.0002 Å °-0.2575 Å °0.2491 Å °-0.0565 Å °0.025 Å °0.3822 Å °0.01 Å °
Refinement TLS groupSelection details: chain A and (not resi 900:901)

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