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- PDB-9dpx: BMP-9 G389S K357R Dimer in Acidic pH -

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Basic information

Entry
Database: PDB / ID: 9dpx
TitleBMP-9 G389S K357R Dimer 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 BMP signaling pathway / positive regulation of bicellular tight junction assembly / blood vessel morphogenesis / negative regulation of endothelial cell migration ...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 BMP signaling pathway / positive regulation of bicellular tight junction assembly / blood vessel morphogenesis / negative regulation of endothelial cell migration / cartilage development / 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 / transcription by RNA polymerase II / intracellular iron ion homeostasis / 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: 2.1 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)12,64312
Polymers12,1771
Non-polymers46611
Water1,24369
1
A: Growth/differentiation factor 2
hetero molecules

A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28624
Polymers24,3542
Non-polymers93222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
MethodPISA
Unit cell
Length a, b, c (Å)71.289, 71.289, 146.379
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

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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.: 6 / 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.: 69 / 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: 3.82 Å3/Da / Density % sol: 67.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1M NaCl , 0.1M Acetic Acid pH 4, 32% Glycerol

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→64.09 Å / Num. obs: 11416 / % possible obs: 100 % / Redundancy: 24.9 % / Biso Wilson estimate: 42.04 Å2 / CC1/2: 0.938 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.075 / Rrim(I) all: 0.276 / Χ2: 1.01 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.2 % / Rmerge(I) obs: 3.389 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 913 / CC1/2: 0.909 / Rpim(I) all: 0.949 / Rrim(I) all: 3.52 / Χ2: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→64.09 Å / SU ML: 0.2397 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 35.2998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 578 5.09 %
Rwork0.2275 10775 -
obs0.2296 11353 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→64.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 21 69 920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164867
X-RAY DIFFRACTIONf_angle_d1.62951175
X-RAY DIFFRACTIONf_chiral_restr0.0958128
X-RAY DIFFRACTIONf_plane_restr0.0147147
X-RAY DIFFRACTIONf_dihedral_angle_d13.6414318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.310.3071390.2632610X-RAY DIFFRACTION99.13
2.31-2.650.30861450.27242655X-RAY DIFFRACTION99.61
2.65-3.330.26611300.23592688X-RAY DIFFRACTION99.65
3.34-64.090.25611640.21062822X-RAY DIFFRACTION99.9
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)
16.10538499450.9703022256542.219437188144.17390136541-0.7100856191369.06883922268-0.7449675128620.1395567218420.52699374127-0.8263365363050.5427712849850.586112958043-0.921941384479-0.966696633731-0.03522947873280.626256106478-0.225947133623-0.06532531054610.5747032298210.1372245852470.3187393774864.9465741665113.4672304275-30.1583451633
25.28676845988-1.061521451480.3844248252777.823833300372.14081100039.72217940901-0.290456385031-0.5263639661640.25744643288-0.248666138872-0.2284318250480.397620515893-0.0604741634744-0.8987369591660.4515408584660.383507419760.151207866192-0.01796627352350.491880095248-0.09402985317450.17503706916419.170829111916.6832657638-7.21567059919
34.318423920080.07044065426092.830632081253.927032756312.235859802677.76387595293-0.1089527519840.41710225506-0.525045412778-0.3965332378530.460974792611-0.06608358594761.190709656210.340446318902-0.3170082621910.608035308148-0.248801224820.0862861415510.4935313750380.008066684563740.2791829784248.545980549233.48032653925-31.6092636632
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 392 )358 - 39235 - 69
33chain 'A' and (resid 393 through 429 )393 - 42970 - 106

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