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- PDB-7ag0: Complex between the bone morphogenetic protein 2 and its antagoni... -

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Basic information

Entry
Database: PDB / ID: 7ag0
TitleComplex between the bone morphogenetic protein 2 and its antagonist Noggin
Components
  • Bone morphogenetic protein 2
  • Noggin
KeywordsCYTOKINE / Bmp-2 / TGF-beta superfamily / cysteine-knot
Function / homology
Function and homology information


neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / notochord morphogenesis / neural plate morphogenesis / cell differentiation in hindbrain / negative regulation of cytokine activity / atrial cardiac muscle tissue morphogenesis / regulation of fibroblast growth factor receptor signaling pathway / ureteric bud formation / cardiac atrium formation ...neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / notochord morphogenesis / neural plate morphogenesis / cell differentiation in hindbrain / negative regulation of cytokine activity / atrial cardiac muscle tissue morphogenesis / regulation of fibroblast growth factor receptor signaling pathway / ureteric bud formation / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of glomerulus development / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / embryonic skeletal joint morphogenesis / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / prostatic bud formation / negative regulation of steroid biosynthetic process / ameloblast differentiation / nodal signaling pathway / positive regulation of extracellular matrix constituent secretion / negative regulation of cardiac muscle cell differentiation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / pharyngeal arch artery morphogenesis / aortic valve development / endoderm formation / telencephalon regionalization / positive regulation of phosphatase activity / positive regulation of odontogenesis / short-term synaptic potentiation / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / ventricular compact myocardium morphogenesis / pericardium development / pituitary gland development / lung vasculature development / BMP receptor complex / membranous septum morphogenesis / embryonic skeletal system development / co-receptor binding / negative regulation of cardiac muscle cell proliferation / negative regulation of cartilage development / telencephalon development / somite development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / positive regulation of odontoblast differentiation / cranial skeletal system development / positive regulation of branching involved in ureteric bud morphogenesis / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / phosphatase activator activity / Transcriptional regulation by RUNX2 / positive regulation of astrocyte differentiation / heart trabecula morphogenesis / Signaling by BMP / cellular response to BMP stimulus / cardiac muscle cell differentiation / axial mesoderm development / cardiac muscle tissue morphogenesis / positive regulation of ossification / astrocyte differentiation / dorsal/ventral pattern formation / motor neuron axon guidance / middle ear morphogenesis / cartilage development / limb development / face morphogenesis / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / exploration behavior / endocardial cushion morphogenesis / smoothened signaling pathway / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / spinal cord development / ventricular septum morphogenesis / lung morphogenesis / negative regulation of SMAD protein signal transduction / negative regulation of fat cell differentiation / cytokine binding / bone mineralization / Formation of paraxial mesoderm / outflow tract morphogenesis / regulation of neuronal synaptic plasticity / positive regulation of osteoblast proliferation / odontogenesis of dentin-containing tooth
Similarity search - Function
Noggin / Noggin / : / 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 ...Noggin / Noggin / : / 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
Bone morphogenetic protein 2 / Noggin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.104 Å
AuthorsRobert, C. / Bruck, F. / Herman, R. / Vandevenne, M. / Filee, P. / Kerff, F. / Matagne, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Walloon Region#16100518 AUTOBMP-2 Belgium
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural analysis of the interaction between human cytokine BMP-2 and the antagonist Noggin reveals molecular details of cell chondrogenesis inhibition.
Authors: Robert, C. / Kerff, F. / Bouillenne, F. / Gavage, M. / Vandevenne, M. / Filee, P. / Matagne, A.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Noggin
B: Bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5056
Polymers36,1372
Non-polymers3684
Water55831
1
A: Noggin
B: Bone morphogenetic protein 2
hetero molecules

A: Noggin
B: Bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,01012
Polymers72,2734
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area10920 Å2
ΔGint-83 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.310, 103.310, 170.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

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Components

#1: Protein Noggin


Mass: 23212.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOG / Plasmid: pET17(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13253
#2: Protein Bone morphogenetic protein 2 / / BMP-2 / Bone morphogenetic protein 2A / BMP-2A


Mass: 12923.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Plasmid: pET17(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12643
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.63 Å3/Da / Density % sol: 66.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.4 M NaKPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 3.1→49.427 Å / Num. obs: 10331 / % possible obs: 99.9 % / Redundancy: 56.6 % / Biso Wilson estimate: 103.29 Å2 / CC1/2: 0.977 / Net I/σ(I): 9.5
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 49.3 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 733 / CC1/2: 0.32 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M4U

1m4u


Resolution: 3.104→49.427 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 514 5.03 %
Rwork0.2321 17448 -
obs0.2345 10266 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.82 Å2 / Biso mean: 101.9559 Å2 / Biso min: 52.18 Å2
Refinement stepCycle: final / Resolution: 3.104→49.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 56 31 2044
Biso mean--114.57 86.67 -
Num. residues----245
LS refinement shellResolution: 3.104→3.2672 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3891 133 -
Rwork0.3844 2481 -
obs--100 %

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