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- PDB-3bmp: HUMAN BONE MORPHOGENETIC PROTEIN-2 (BMP-2) -

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Basic information

Entry
Database: PDB / ID: 3bmp
TitleHUMAN BONE MORPHOGENETIC PROTEIN-2 (BMP-2)
ComponentsPROTEIN (BONE MORPHOGENETIC PROTEIN 2 (BMP-2))
KeywordsCYTOKINE / BONE MORPHOGENETIC PROTEIN / CYSTIN-KNOT / TGFB-FAMILY
Function / homology
Function and homology information


cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development / positive regulation of extracellular matrix constituent secretion / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / negative regulation of steroid biosynthetic process ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development / positive regulation of extracellular matrix constituent secretion / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification / mesenchymal cell proliferation involved in ureteric bud development / enzyme activator complex / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / negative regulation of cardiac muscle cell differentiation / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / negative regulation of insulin-like growth factor receptor signaling pathway / ameloblast differentiation / aortic valve development / pericardium development / telencephalon regionalization / heart induction / positive regulation of cartilage development / positive regulation of odontogenesis / positive regulation of peroxisome proliferator activated receptor signaling pathway / BMP receptor complex / proteoglycan metabolic process / co-receptor binding / lung vasculature development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / telencephalon development / BMP receptor binding / positive regulation of bone mineralization involved in bone maturation / positive regulation of odontoblast differentiation / phosphatase activator activity / Transcriptional regulation by RUNX2 / endocardial cushion formation / positive regulation of astrocyte differentiation / cellular response to BMP stimulus / Signaling by BMP / cardiac muscle cell differentiation / astrocyte differentiation / cardiac muscle tissue morphogenesis / positive regulation of ossification / positive regulation of p38MAPK cascade / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / Molecules associated with elastic fibres / branching involved in ureteric bud morphogenesis / positive regulation of osteoblast proliferation / negative regulation of fat cell differentiation / bone mineralization / odontogenesis of dentin-containing tooth / inner ear development / negative regulation of cell cycle / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / cell fate commitment / positive regulation of Wnt signaling pathway / chondrocyte differentiation / positive regulation of fat cell differentiation / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / osteoclast differentiation / animal organ morphogenesis / protein serine/threonine kinase activator activity / cytokine activity / skeletal system development / response to bacterium / growth factor activity / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of canonical Wnt signaling pathway / bone development / protein destabilization / positive regulation of miRNA transcription / positive regulation of protein phosphorylation / Regulation of RUNX2 expression and activity / osteoblast differentiation / cell-cell signaling / heart development / in utero embryonic development / transcription by RNA polymerase II / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / cilium / positive regulation of cell migration / positive regulation of apoptotic process / inflammatory response / signaling receptor binding / negative regulation of cell population proliferation
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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal ...: / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsScheufler, C. / Sebald, W. / Huelsmeyer, M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of human bone morphogenetic protein-2 at 2.7 A resolution.
Authors: Scheufler, C. / Sebald, W. / Hulsmeyer, M.
#1: Journal: Eur.J.Biochem. / Year: 1996
Title: Human Bone Morphogenetic Protein 2 Contains a Heparin-Binding Site which Modifies its Biological Activity
Authors: Ruppert, R. / Hoffmann, E. / Sebald, W.
History
DepositionMar 12, 1999Deposition site: BNL / Processing site: RCSB
SupersessionMar 12, 2000ID: 2BMP
Revision 1.0Mar 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BONE MORPHOGENETIC PROTEIN 2 (BMP-2))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0422
Polymers12,9241
Non-polymers1181
Water59433
1
A: PROTEIN (BONE MORPHOGENETIC PROTEIN 2 (BMP-2))
hetero molecules

A: PROTEIN (BONE MORPHOGENETIC PROTEIN 2 (BMP-2))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0844
Polymers25,8482
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area3470 Å2
ΔGint-56 kcal/mol
Surface area11150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.440, 91.440, 107.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE NATIVE HOMODIMERIC FORM OF BMP-2 IS BUILT BY CRYSTALLOGRAPHIC SYMMETRY. THE MONOMERS ARE LINKED VIA A CYSTINE BRIDGE (CYS78 FROM BOTH SUBUNITS)

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Components

#1: Protein PROTEIN (BONE MORPHOGENETIC PROTEIN 2 (BMP-2))


Mass: 12923.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12643
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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 Å3/Da / Density % sol: 59 %
Crystal growpH: 5.4
Details: CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 100 MM LITHIUM SULFATE, 12% TERT-BUTANOL, 50 MM CITRATE, PH 5.4
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
220 mMacetate1drop
350 mMcitrate1reservoir
4100 mMlithium sulfate1reservoir
512 %(v/v)tertbutanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 30, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 4647 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 5.4 / % possible all: 82.2
Reflection shell
*PLUS
% possible obs: 82.2 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TFG

1tfg


Resolution: 2.7→25 Å / Rfactor Rfree error: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 296 6 %RANDOM
Rwork0.242 ---
obs-4647 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å24.1 Å20 Å2
2--0.85 Å20 Å2
3----1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 8 33 874
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.411.5
X-RAY DIFFRACTIONx_mcangle_it2.552
X-RAY DIFFRACTIONx_scbond_it1.512
X-RAY DIFFRACTIONx_scangle_it2.472.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 42 6 %
Rwork0.298 638 -
obs--84.4 %
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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