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- PDB-9dpr: BMP-9 Wild-Type Dimer with Radiation Damage in Acidic pH -

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Basic information

Entry
Database: PDB / ID: 9dpr
TitleBMP-9 Wild-Type Dimer with Radiation Damage in Acidic 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: 2.61 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

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,63515
Polymers12,1191
Non-polymers51614
Water1,08160
1
A: Growth/differentiation factor 2
hetero molecules

A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,26930
Polymers24,2382
Non-polymers1,03128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1/2,-z+1/41
MethodPISA
Unit cell
Length a, b, c (Å)71.044, 71.044, 145.564
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-506-

CL

21A-650-

HOH

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Components

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


Mass: 12118.971 Da / Num. of mol.: 1 / Mutation: A321S
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / 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.: 60 / 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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 1M NaCl, 3.5% PEG8K, 0.3M Sodium Citrate pH 3.5

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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: Apr 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→41.34 Å / Num. obs: 5804 / % possible obs: 98 % / Redundancy: 5.4 % / Biso Wilson estimate: 50.38 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.301 / Rpim(I) all: 0.188 / Rrim(I) all: 0.357 / Χ2: 1.08 / Net I/σ(I): 4.9
Reflection shellResolution: 2.61→2.73 Å / Redundancy: 5.5 % / Rmerge(I) obs: 2.521 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 684 / CC1/2: 0.265 / Rpim(I) all: 1.61 / Rrim(I) all: 3.017 / Χ2: 0.93 / % possible all: 97.9
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: 2.61→41.34 Å / SU ML: 0.3762 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 31.82
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 306 5.28 %
Rwork0.2122 5492 -
obs0.2153 5798 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.73 Å2
Refinement stepCycle: LAST / Resolution: 2.61→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 19 60 905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071854
X-RAY DIFFRACTIONf_angle_d1.00711157
X-RAY DIFFRACTIONf_chiral_restr0.056126
X-RAY DIFFRACTIONf_plane_restr0.0053145
X-RAY DIFFRACTIONf_dihedral_angle_d9.5626311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-3.290.33441440.26212696X-RAY DIFFRACTION97.73
3.29-41.340.24531620.19432796X-RAY DIFFRACTION96.04
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)
17.79715488233-1.211430017940.229176691976.03750891657-3.441812534519.49637039040.3609558541770.4722812307480.411157162435-0.131192181053-0.492962906059-0.363855608668-0.7995290092480.7858666480710.1024324414850.4059852093230.07917808245730.06901292678830.2940303583580.009305167754280.469297071514-22.1617023696-4.73812343616.37555358455
23.810626633972.28918237151.998746657011.602253242270.04555754715466.95311456826-0.331223637622-0.3902343015411.075644579420.952889748507-0.7488590959750.0499372884603-1.840354510390.0869536725703-0.1423785204420.777653657825-0.129531505882-0.2084103966120.4349394447380.01311325377970.600668791737-22.5541124253-12.214400795529.7815422977
34.08458964674-0.2562608213012.009453548143.99383426965-2.226477806035.953018228540.28489287688-0.533844999510.195250691215-0.42565804474-0.215255551557-0.1600023580850.05425537475970.3470608718660.3333894130810.334545996089-0.02250672873590.004950959048450.251026110681-0.04570909950470.322724213319-18.6532104797-21.520595062626.851722604
43.00830315730.7472134066-0.6933707565583.23478213276-0.4077134956992.563389863380.5121362206210.467395930241-0.0860075885193-0.563969718486-0.1357842201340.6447152671270.118433594125-0.627854952399-0.1912525598550.4700120534560.224606417344-0.06624866547240.369328219684-0.09179539963740.423546545041-32.9639066095-7.809961656572.78949177234
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 324 through 357 )324 - 3571 - 34
22chain 'A' and (resid 358 through 371 )358 - 37135 - 48
33chain 'A' and (resid 372 through 397 )372 - 39749 - 74
44chain 'A' and (resid 398 through 429 )398 - 42975 - 106

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