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- PDB-9dpw: BMP-9 K357R G389S Dimer With Radiation Damage in Neutral pH -

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Basic information

Entry
Database: PDB / ID: 9dpw
TitleBMP-9 K357R G389S Dimer With Radiation Damage in Neutral pH
ComponentsGrowth/differentiation factor 2
KeywordsSIGNALING PROTEIN / BMP / bone morphogenetic protein / TGF-beta family
Function / homology
Function and homology information


positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of bicellular tight junction assembly / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis ...positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of bicellular tight junction assembly / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / negative regulation of DNA replication / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / BMP signaling pathway / vasculogenesis / positive regulation of endothelial cell proliferation / ossification / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / negative regulation of cell growth / positive regulation of angiogenesis / osteoblast differentiation / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region
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
Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,74915
Polymers12,1771
Non-polymers57214
Water82946
1
A: Growth/differentiation factor 2
hetero molecules

A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,49830
Polymers24,3542
Non-polymers1,14428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
MethodPISA
Unit cell
Length a, b, c (Å)71.100, 71.100, 145.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-505-

CL

21A-635-

HOH

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Components

#1: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12177.011 Da / Num. of mol.: 1 / Mutation: A321S, K357R, G389S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Plasmid: pcdna3.1 / Cell line (production host): expi293 (Invitrogen) / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): embryonic / References: UniProt: Q9UK05
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1M NaCl, 22-26% glycerol, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→40.08 Å / Num. obs: 5360 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 52.19 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.443 / Rpim(I) all: 0.247 / Rrim(I) all: 0.511 / Χ2: 0.97 / Net I/σ(I): 4.2
Reflection shellResolution: 2.71→2.84 Å / Redundancy: 7.4 % / Rmerge(I) obs: 4.532 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 706 / CC1/2: 0.309 / Rpim(I) all: 2.505 / Rrim(I) all: 5.208 / Χ2: 1.04 / % possible all: 99.6
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→40.08 Å / SU ML: 0.3862 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 20.0512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2986 259 4.85 %
Rwork0.2235 5076 -
obs0.227 5335 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.79 Å2
Refinement stepCycle: LAST / Resolution: 2.71→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 24 46 896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093859
X-RAY DIFFRACTIONf_angle_d1.35651163
X-RAY DIFFRACTIONf_chiral_restr0.0802127
X-RAY DIFFRACTIONf_plane_restr0.0105145
X-RAY DIFFRACTIONf_dihedral_angle_d12.9849314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-3.410.31671220.26862492X-RAY DIFFRACTION99.39
3.42-40.080.29231370.20582584X-RAY DIFFRACTION98.77

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