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- PDB-6omn: Glycosylated BMP2 homodimer -

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Basic information

Entry
Database: PDB / ID: 6omn
TitleGlycosylated BMP2 homodimer
ComponentsBone morphogenetic protein 2
KeywordsCYTOKINE / BMP / Bone Mophogenetic Protein
Function / homology
Function and homology information


cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / ameloblast differentiation / 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 / aortic valve development / telencephalon regionalization / positive regulation of odontogenesis / positive regulation of phosphatase activity / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / pericardium development / lung vasculature development / BMP receptor complex / co-receptor binding / telencephalon development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / positive regulation of odontoblast differentiation / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / phosphatase activator activity / Transcriptional regulation by RUNX2 / positive regulation of astrocyte differentiation / Signaling by BMP / cellular response to BMP stimulus / cardiac muscle cell differentiation / cardiac muscle tissue morphogenesis / positive regulation of ossification / astrocyte differentiation / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / endocardial cushion morphogenesis / branching involved in ureteric bud morphogenesis / negative regulation of fat cell differentiation / bone mineralization / positive regulation of osteoblast proliferation / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / inner ear development / cellular response to organic cyclic compound / negative regulation of cell cycle / positive regulation of Wnt signaling pathway / epithelial to mesenchymal transition / positive regulation of fat cell differentiation / cell fate commitment / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / protein serine/threonine kinase activator activity / osteoclast differentiation / negative regulation of MAP kinase activity / skeletal system development / cytokine activity / animal organ morphogenesis / negative regulation of smooth muscle cell proliferation / response to bacterium / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / protein destabilization / bone development / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / osteoblast differentiation / Regulation of RUNX2 expression and activity / positive regulation of protein binding / cell-cell signaling / heart development / in utero embryonic development / transcription by RNA polymerase II / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / positive regulation of apoptotic process
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
Bone morphogenetic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsJuo, Z.S. / Seeherman, H.
CitationJournal: Sci Transl Med / Year: 2019
Title: A BMP/activin A chimera is superior to native BMPs and induces bone repair in nonhuman primates when delivered in a composite matrix.
Authors: Seeherman, H.J. / Berasi, S.P. / Brown, C.T. / Martinez, R.X. / Juo, Z.S. / Jelinsky, S. / Cain, M.J. / Grode, J. / Tumelty, K.E. / Bohner, M. / Grinberg, O. / Orr, N. / Shoseyov, O. / ...Authors: Seeherman, H.J. / Berasi, S.P. / Brown, C.T. / Martinez, R.X. / Juo, Z.S. / Jelinsky, S. / Cain, M.J. / Grode, J. / Tumelty, K.E. / Bohner, M. / Grinberg, O. / Orr, N. / Shoseyov, O. / Eyckmans, J. / Chen, C. / Morales, P.R. / Wilson, C.G. / Vanderploeg, E.J. / Wozney, J.M.
History
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Bone morphogenetic protein 2
F: Bone morphogenetic protein 2
G: Bone morphogenetic protein 2
H: Bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4438
Polymers48,8004
Non-polymers3,6434
Water82946
1
E: Bone morphogenetic protein 2
F: Bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2224
Polymers24,4002
Non-polymers1,8222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint12 kcal/mol
Surface area12580 Å2
MethodPISA
2
G: Bone morphogenetic protein 2
H: Bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2224
Polymers24,4002
Non-polymers1,8222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint13 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.743, 62.743, 126.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Bone morphogenetic protein 2 / BMP-2 / Bone morphogenetic protein 2A / BMP-2A


Mass: 12200.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P12643
#2: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100mM TrisHCl pH 8.5, 100mM NaCl, 12% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→41.2 Å / Num. obs: 15473 / % possible obs: 98.88 % / Redundancy: 4 % / Biso Wilson estimate: 75.99 Å2 / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→41.2 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.8842 / SU R Cruickshank DPI: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.694 / SU Rfree Blow DPI: 0.304 / SU Rfree Cruickshank DPI: 0.315
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 776 5.02 %RANDOM
Rwork0.175 ---
obs0.1786 15473 98.88 %-
Displacement parametersBiso mean: 70.78 Å2
Baniso -1Baniso -2Baniso -3
1-12.318 Å20 Å20 Å2
2--12.318 Å20 Å2
3----24.636 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: 1 / Resolution: 2.68→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 61 46 3412
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013675HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.295052HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1192SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes512HARMONIC5
X-RAY DIFFRACTIONt_it3675HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion21.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion513SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3768SEMIHARMONIC4
LS refinement shellResolution: 2.68→2.87 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3483 130 4.77 %
Rwork0.1947 2596 -
all0.2021 2726 -
obs--98.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6503-2.11020.67372.2714-0.45020.8688-0.03940.1203-0.0664-0.0708-0.0096-0.06510.09190.18120.0489-0.1820.01210.0358-0.16450.00060.012-11.630125.5727-1.0582
26.82871.1409-1.68850.5445-0.88911.3009-0.1247-0.01480.10670.0699-0.0273-0.1589-0.0060.02470.152-0.20490.0399-0.0159-0.1947-0.03610.08995.620426.30435.6209
37.42760.024-0.46990.6397-0.24560.539-0.15-0.1276-0.08580.04340.13840.2619-0.09280.02820.0115-0.23990.0149-0.0007-0.1598-0.03630.0525-5.954657.2501-6.5332
46.7371-1.87761.29321.352-0.38891.7873-0.13630.19-0.35580.06440.07690.0327-0.1603-0.0120.0595-0.2691-0.0296-0.0094-0.1894-0.04210.021710.955851.5539-11.4227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ E|* }
2X-RAY DIFFRACTION2{ F|* }
3X-RAY DIFFRACTION3{ G|* }
4X-RAY DIFFRACTION4{ H|* }

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