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- PDB-8e3g: BMP2/GDF5 heterodimer -

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Basic information

Entry
Database: PDB / ID: 8e3g
TitleBMP2/GDF5 heterodimer
Components
  • Bone morphogenetic protein 2
  • Growth/differentiation factor 5
KeywordsSIGNALING PROTEIN / Cystine-knot Growth factor Heterodimer
Function / homology
Function and homology information


ossification involved in bone remodeling / 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 ...ossification involved in bone remodeling / 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 / forelimb morphogenesis / 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 / chondroblast differentiation / BMP binding / hindlimb morphogenesis / heart induction / negative regulation of mesenchymal cell apoptotic process / positive regulation of cartilage development / positive regulation of odontogenesis / positive regulation of peroxisome proliferator activated receptor signaling pathway / positive regulation of chondrocyte differentiation / BMP receptor complex / proteoglycan metabolic process / co-receptor binding / mesenchymal cell apoptotic process / lung vasculature development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / positive regulation of bone mineralization involved in bone maturation / positive regulation of odontoblast differentiation / telencephalon development / 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 / positive regulation of BMP signaling pathway / astrocyte differentiation / cardiac muscle tissue morphogenesis / positive regulation of ossification / positive regulation of p38MAPK cascade / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / atrioventricular valve morphogenesis / Molecules associated with elastic fibres / endocardial cushion morphogenesis / branching involved in ureteric bud morphogenesis / positive regulation of osteoblast proliferation / negative regulation of fat cell differentiation / bone mineralization / odontogenesis of dentin-containing tooth / negative regulation of cell cycle / inner ear development / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / regulation of multicellular organism growth / cell fate commitment / chondrocyte differentiation / positive regulation of Wnt signaling pathway / response to mechanical stimulus / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / positive regulation of fat cell differentiation / BMP signaling pathway / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / 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 / negative regulation of epithelial cell 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 / 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 / Growth/differentiation factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGipson, G.R. / Nolan, K.T. / Thompson, T.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM134923-02 United States
CitationJournal: Bmc Biol. / Year: 2023
Title: Formation and characterization of BMP2/GDF5 and BMP4/GDF5 heterodimers.
Authors: Gipson, G.R. / Nolan, K. / Kattamuri, C. / Kenny, A.P. / Agricola, Z. / Edwards, N.A. / Zinski, J. / Czepnik, M. / Mullins, M.C. / Zorn, A.M. / Thompson, T.B.
History
DepositionAug 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein 2
B: Growth/differentiation factor 5
C: Bone morphogenetic protein 2
D: Growth/differentiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5059
Polymers53,0454
Non-polymers4605
Water00
1
A: Bone morphogenetic protein 2
B: Growth/differentiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7074
Polymers26,5222
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-30 kcal/mol
Surface area11620 Å2
MethodPISA
2
C: Bone morphogenetic protein 2
D: Growth/differentiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7995
Polymers26,5222
Non-polymers2763
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-33 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.321, 98.321, 174.783
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 12923.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Production host: Escherichia coli (E. coli) / References: UniProt: P12643
#2: Protein Growth/differentiation factor 5 / GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 ...GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 / Lipopolysaccharide-associated protein 4 / LAP-4 / LPS-associated protein 4 / Radotermin


Mass: 13598.638 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF5, BMP14, CDMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43026
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN
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: 4.6 Å3/Da / Density % sol: 73.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris, magnesium formate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→76.6 Å / Num. obs: 24734 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 56.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.055 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2428 / CC1/2: 0.709 / Rpim(I) all: 0.426

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Processing

Software
NameVersionClassification
REFMAC1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAQ, 1REU

1waq

1reu


Resolution: 2.8→76.55 Å / SU ML: 0.3555 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.5825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 1212 4.9 %
Rwork0.1932 23506 -
obs0.1951 24718 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.68 Å2
Refinement stepCycle: LAST / Resolution: 2.8→76.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 30 0 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01473411
X-RAY DIFFRACTIONf_angle_d1.33634639
X-RAY DIFFRACTIONf_chiral_restr0.062506
X-RAY DIFFRACTIONf_plane_restr0.0101600
X-RAY DIFFRACTIONf_dihedral_angle_d15.56281246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.910.33641440.30462546X-RAY DIFFRACTION100
2.91-3.040.2951390.27272562X-RAY DIFFRACTION100
3.04-3.210.29381430.25052554X-RAY DIFFRACTION100
3.21-3.410.26551420.21262597X-RAY DIFFRACTION100
3.41-3.670.2691360.19152565X-RAY DIFFRACTION100
3.67-4.040.18221510.17432593X-RAY DIFFRACTION100
4.04-4.620.19081200.14372632X-RAY DIFFRACTION100
4.62-5.820.19571130.1642678X-RAY DIFFRACTION100
5.83-76.550.23791240.20292779X-RAY DIFFRACTION99.45
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)
13.720849204262.31978133431-0.7364369947482.15670735601-0.6247236943881.280688085140.0681524580731-0.5570174596940.03733224670840.302295167861-0.166692914831-0.0752526098317-0.165001387703-0.001584712018920.08416901995230.3962519941090.127337318915-0.01649051865050.5664024578720.01080963318080.37520184229430.0874587038-42.422918083-46.4252638303
25.515850775891.15280871496-2.456783080391.16525128541-0.2756740741461.77594930211-0.4275931388270.2437959352580.284100102686-0.176305022990.230072815260.0867998571680.0110085640045-0.08031373181510.1508228088910.338238960140.0858753267819-0.03843276226390.5613461303580.01006533579580.41370474236443.5884030503-37.0242094177-57.5786994025
31.104298837350.900486115883-0.5833874374335.69252171416-1.779215979040.656118700756-0.07076729295320.132470844517-0.105445858212-0.835307813229-0.06646597385520.003867379660310.2946096697950.04047438274190.1542580264250.5685140748690.1814241991880.03175991293130.5013722504230.04375859366340.36899301469252.06496630044.05490057627-40.0130890637
40.158071229907-0.795896175480.199391488446.42707721331-1.297748074590.5221618065110.07127715315690.09789192230380.009955091288980.0541203632573-0.176662978510.3560635538740.0114509016117-0.09398159032910.09996384946670.5769653851630.2064771576510.07144005748540.4846901846730.07845334767930.495650855450.576017187-12.3735949347-31.860982009
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 11:114)AA11 - 1141 - 104
22(chain B and resseq 16:120)BC16 - 1201 - 105
33(chain C and resseq 11:114)CE11 - 1141 - 104
44(chain D and resseq 16:120)DG16 - 1201 - 105

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