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- PDB-6omo: Human BMP6 homodimer -

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Basic information

Entry
Database: PDB / ID: 6omo
TitleHuman BMP6 homodimer
ComponentsBone morphogenetic protein 6
KeywordsCYTOKINE / BMP / bone morphogenetic protein
Function / homology
Function and homology information


positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / enzyme activator complex / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / eye development / type B pancreatic cell development / BMP receptor binding / cellular response to BMP stimulus ...positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / enzyme activator complex / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / eye development / type B pancreatic cell development / BMP receptor binding / cellular response to BMP stimulus / endochondral ossification / male genitalia development / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of vascular permeability / positive regulation of lipopolysaccharide-mediated signaling pathway / cartilage development / response to magnesium ion / positive regulation of intracellular signal transduction / positive regulation of SMAD protein signal transduction / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to retinoic acid / response to glucocorticoid / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / positive regulation of epithelial cell proliferation / cytokine activity / response to activity / kidney development / skeletal system development / cellular response to iron ion / positive regulation of protein secretion / growth factor activity / bone development / multicellular organismal-level iron ion homeostasis / cellular response to mechanical stimulus / neuron differentiation / osteoblast differentiation / vesicle / intracellular iron ion homeostasis / immune response / inflammatory response / protein heterodimerization activity / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space
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
ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / Bone morphogenetic protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / chem_comp ...atom_site / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Bone morphogenetic protein 6
J: Bone morphogenetic protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,77212
Polymers23,5532
Non-polymers1,21810
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint4 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.398, 97.398, 85.644
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules IJ

#1: Protein Bone morphogenetic protein 6 / BMP-6 / VG-1-related protein / VGR-1


Mass: 11776.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP6, VGR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22004

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 47 molecules

#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.89 Å3/Da / Density % sol: 74.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris HCl 8.0, 15% 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: MAC Science DIP-320 / Detector: IMAGE PLATE / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.7 Å / Num. obs: 14720 / % possible obs: 99.49 % / Redundancy: 4 % / Biso Wilson estimate: 79.1 Å2 / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9226 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.271 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.219
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 745 5.06 %RANDOM
Rwork0.2155 ---
obs0.217 14720 99.49 %-
Displacement parametersBiso mean: 68.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.3979 Å20 Å20 Å2
2--1.3979 Å20 Å2
3----2.7958 Å2
Refine analyzeLuzzati coordinate error obs: 0.344 Å
Refinement stepCycle: 1 / Resolution: 2.8→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 52 39 1737
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011774HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.32414HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d560SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes254HARMONIC5
X-RAY DIFFRACTIONt_it1774HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion22.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion232SEMIHARMONIC5
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_contact1806SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.81 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.282 160 5.47 %
Rwork0.2285 2764 -
all0.2313 2924 -
obs--99.49 %

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