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- PDB-9dpy: BMP-10 with BMP-9 Crystal Contacts -

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Basic information

Entry
Database: PDB / ID: 9dpy
TitleBMP-10 with BMP-9 Crystal Contacts
ComponentsBone morphogenetic protein 10
KeywordsSIGNALING PROTEIN / BMP / bone morphogenetic protein / TGF-beta family
Function / homology
Function and homology information


regulation of cardiac muscle hypertrophy in response to stress / positive regulation of sarcomere organization / positive regulation of cell proliferation involved in heart morphogenesis / atrial cardiac muscle tissue morphogenesis / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway ...regulation of cardiac muscle hypertrophy in response to stress / positive regulation of sarcomere organization / positive regulation of cell proliferation involved in heart morphogenesis / atrial cardiac muscle tissue morphogenesis / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway / receptor serine/threonine kinase binding / adult heart development / heart trabecula formation / negative regulation of endothelial cell migration / sarcomere organization / Molecules associated with elastic fibres / ventricular cardiac muscle tissue morphogenesis / positive regulation of cardiac muscle hypertrophy / positive regulation of SMAD protein signal transduction / cardiac muscle cell proliferation / regulation of cardiac muscle contraction / BMP signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of cell migration / cytokine activity / growth factor activity / kidney development / negative regulation of cell growth / hormone activity / Z disc / cell adhesion / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular region / cytoplasm
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
PHOSPHATE ION / Bone morphogenetic protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSchwartze, T.A. / Hinck, A.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58670 United States
Department of Defense (DOD, United States)W81XWH-17-1-0429 United States
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10.
Authors: Schwartze, T.A. / Morosky, S.A. / Rosato, T.L. / Henrickson, A. / Lin, G. / Hinck, C.S. / Taylor, A.B. / Olsen, S.K. / Calero, G. / Demeler, B. / Roman, B.L. / Hinck, A.P.
History
DepositionSep 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bone morphogenetic protein 10
B: Bone morphogenetic protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,60717
Polymers24,3262
Non-polymers1,28115
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Covalent dimer observed by SDS Gel
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-97 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.752, 123.038, 120.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-501-

PO4

21B-645-

HOH

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Components

#1: Protein Bone morphogenetic protein 10 / BMP-10


Mass: 12163.132 Da / Num. of mol.: 2 / Mutation: N357F, Y358F, A374T, Y409L, F411Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Plasmid: pcdna3.1 / Cell line (production host): expi293 (Invitrogen) / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): embryonic / References: UniProt: O95393
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25% (v/v) 1,2-propanediol, 100 mM sodium phosphate dibasic/potassium phosphate monobasic pH 6.2, 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.77→61.52 Å / Num. obs: 31025 / % possible obs: 98.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 35.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.04 / Rrim(I) all: 0.088 / Χ2: 1.05 / Net I/σ(I): 12.2
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 8.9 % / Rmerge(I) obs: 2.426 / Mean I/σ(I) obs: 1 / Num. unique obs: 4391 / CC1/2: 0.531 / Rpim(I) all: 1.237 / Rrim(I) all: 2.727 / Χ2: 0.84 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→61.52 Å / SU ML: 0.2709 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.6611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2512 1995 6.44 %
Rwork0.2141 28970 -
obs0.2165 30965 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.29 Å2
Refinement stepCycle: LAST / Resolution: 1.77→61.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 67 144 1875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831762
X-RAY DIFFRACTIONf_angle_d0.96212398
X-RAY DIFFRACTIONf_chiral_restr0.0542254
X-RAY DIFFRACTIONf_plane_restr0.008288
X-RAY DIFFRACTIONf_dihedral_angle_d11.8129632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.56671360.56351972X-RAY DIFFRACTION95.34
1.81-1.860.54571410.48872038X-RAY DIFFRACTION97.98
1.86-1.920.40751370.4212018X-RAY DIFFRACTION97.78
1.92-1.980.40041410.36252048X-RAY DIFFRACTION97.94
1.98-2.050.35841400.31732035X-RAY DIFFRACTION97.67
2.05-2.130.33031420.27332045X-RAY DIFFRACTION98.07
2.13-2.230.28351390.25742030X-RAY DIFFRACTION98.41
2.23-2.350.27411430.22262071X-RAY DIFFRACTION98.71
2.35-2.490.21731430.1982077X-RAY DIFFRACTION98.45
2.49-2.690.24851430.20342077X-RAY DIFFRACTION98.19
2.69-2.960.2361440.19092083X-RAY DIFFRACTION99.29
2.96-3.390.21351450.18062104X-RAY DIFFRACTION99.47
3.39-4.270.19811480.17312154X-RAY DIFFRACTION99.48
4.27-61.520.24351530.19712218X-RAY DIFFRACTION98.92

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