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- PDB-1m4u: Crystal structure of Bone Morphogenetic Protein-7 (BMP-7) in comp... -

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Basic information

Entry
Database: PDB / ID: 1m4u
TitleCrystal structure of Bone Morphogenetic Protein-7 (BMP-7) in complex with the secreted antagonist Noggin
Components
  • Bone Morphogenetic Protein-7
  • Noggin
KeywordsHORMONE/GROWTH FACTOR / NOGGIN / BMP ANTAGONIST / BMP-7 / BONE MORPHOGENETIC PROTEIN / CYSTINE KNOT / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / notochord morphogenesis / negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / neural plate morphogenesis / positive regulation of hyaluranon cable assembly ...neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / notochord morphogenesis / negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / neural plate morphogenesis / positive regulation of hyaluranon cable assembly / cell differentiation in hindbrain / negative regulation of cytokine activity / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / regulation of fibroblast growth factor receptor signaling pathway / ureteric bud formation / negative regulation of striated muscle cell apoptotic process / embryonic skeletal joint morphogenesis / neural fold elevation formation / prostatic bud formation / nodal signaling pathway / positive regulation of glomerulus development / atrial cardiac muscle tissue morphogenesis / endoderm formation / embryonic camera-type eye morphogenesis / metanephric mesenchymal cell proliferation involved in metanephros development / mesenchyme development / ameloblast differentiation / positive regulation of epithelial cell differentiation / pharyngeal arch artery morphogenesis / short-term synaptic potentiation / monocyte aggregation / pituitary gland development / ventricular compact myocardium morphogenesis / allantois development / mesonephros development / membranous septum morphogenesis / embryonic skeletal system development / negative regulation of cartilage development / regulation of removal of superoxide radicals / negative regulation of cardiac muscle cell proliferation / hindbrain development / mesenchymal cell differentiation / pericardium morphogenesis / somite development / BMP receptor binding / cranial skeletal system development / endocardial cushion formation / positive regulation of branching involved in ureteric bud morphogenesis / pharyngeal system development / heart trabecula morphogenesis / cellular response to BMP stimulus / Signaling by BMP / branching involved in salivary gland morphogenesis / embryonic pattern specification / metanephros development / response to vitamin D / negative regulation of mitotic nuclear division / axial mesoderm development / dorsal/ventral pattern formation / motor neuron axon guidance / positive regulation of heterotypic cell-cell adhesion / negative regulation of non-canonical NF-kappaB signal transduction / embryonic limb morphogenesis / cardiac muscle tissue development / limb development / face morphogenesis / cartilage development / exploration behavior / middle ear morphogenesis / positive regulation of dendrite development / ureteric bud development / Molecules associated with elastic fibres / regulation of branching involved in prostate gland morphogenesis / embryonic digit morphogenesis / branching morphogenesis of an epithelial tube / smoothened signaling pathway / ventricular septum morphogenesis / negative regulation of SMAD protein signal transduction / spinal cord development / cardiac septum morphogenesis / Formation of paraxial mesoderm / cytokine binding / negative regulation of NF-kappaB transcription factor activity / lung morphogenesis / dendrite development / odontogenesis of dentin-containing tooth / outflow tract morphogenesis / negative regulation of astrocyte differentiation / regulation of neuronal synaptic plasticity / negative regulation of apoptotic signaling pathway / mesoderm formation / negative regulation of cell cycle / somatic stem cell population maintenance / negative regulation of BMP signaling pathway / positive regulation of SMAD protein signal transduction / negative regulation of Notch signaling pathway / negative regulation of neuron differentiation / fibroblast growth factor receptor signaling pathway
Similarity search - Function
Helix hairpin bin / 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 ...Helix hairpin bin / 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Helix Hairpins / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Bone morphogenetic protein 7 / Noggin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.42 Å
AuthorsGroppe, J. / Greenwald, J. / Wiater, E. / Rodriguez-Leon, J. / Economides, A.N. / Kwiatkowski, W. / Affolter, M. / Vale, W.W. / Izpisua-Belmonte, J.C. / Choe, S.
Citation
Journal: Nature / Year: 2002
Title: Structural Basis of BMP Signalling Inhibition by the Cystine Knot Protein Noggin
Authors: Groppe, J. / Greenwald, J. / Wiater, E. / Rodriguez-Leon, J. / Economides, A.N. / Kwiatkowski, W. / Affolter, M. / Vale, W.W. / Izpisua-Belmonte, J.C. / Choe, S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Three-dimensional structure of recombinant human osteogenic protein 1: Structural paradigm for the transforming growth factor beta superfamily
Authors: Griffith, D.L. / Keck, P.C. / Sampath, T.K. / Rueger, D.C. / Carlson, W.D.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
L: Bone Morphogenetic Protein-7
A: Noggin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3373
Polymers38,9132
Non-polymers4241
Water82946
1
L: Bone Morphogenetic Protein-7
A: Noggin
hetero molecules

L: Bone Morphogenetic Protein-7
A: Noggin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6746
Polymers77,8254
Non-polymers8492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area12100 Å2
ΔGint-63 kcal/mol
Surface area34570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.834, 99.834, 150.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: -y,-x,-z+.5

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Components

#1: Protein Bone Morphogenetic Protein-7 / BMP-7 / Osteogenic protein 1 / OP-1


Mass: 15699.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DHFR- / Gene: BMP7 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P18075
#2: Protein Noggin


Mass: 23212.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: high copy number derivative of pBR322 with a lacUV5 promoter
Gene: NOG / Plasmid: pRG301 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 lacIq / References: UniProt: Q13253
#3: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 4.81 Å3/Da / Density % sol: 74.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.6 M disodium, 1.0 M monopotassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.6 Mdisodium1reservoir
31.0 Mmonopotassium phosphate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.04888, 0.91987, 0.91957, 0.88557
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2001
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.048881
20.919871
30.919571
40.885571
ReflectionResolution: 2.42→60 Å / Num. all: 29713 / Num. obs: 28463 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.054
Reflection shellResolution: 2.42→2.483 Å / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 60 Å / Num. measured all: 92080 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Lowest resolution: 2.48 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.331

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
REFMAC5refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.42→60.05 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.409 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27303 1441 5.1 %RANDOM
Rwork0.24078 ---
obs0.24243 27000 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.42→60.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 28 46 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0212590
X-RAY DIFFRACTIONr_bond_other_d0.0020.022288
X-RAY DIFFRACTIONr_angle_refined_deg3.0341.973515
X-RAY DIFFRACTIONr_angle_other_deg1.34535346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1733308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.63215476
X-RAY DIFFRACTIONr_chiral_restr0.2010.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022820
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02520
X-RAY DIFFRACTIONr_nbd_refined0.280.3637
X-RAY DIFFRACTIONr_nbd_other0.2820.32444
X-RAY DIFFRACTIONr_nbtor_other0.3430.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.5174
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2260.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.372
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.3187
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.513
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0620.51
X-RAY DIFFRACTIONr_mcbond_it1.781.51557
X-RAY DIFFRACTIONr_mcangle_it3.22722515
X-RAY DIFFRACTIONr_scbond_it4.11631033
X-RAY DIFFRACTIONr_scangle_it6.6024.51000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 120
Rwork0.287 2026
Refinement
*PLUS
Lowest resolution: 60 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.035
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg3

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