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- PDB-9dpp: BMP-9 Wild-Type Dimer in Acidic pH -

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Basic information

Entry
Database: PDB / ID: 9dpp
TitleBMP-9 Wild-Type 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 / protein serine/threonine kinase activator activity / negative regulation of angiogenesis / 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: 2.12 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)12,73717
Polymers12,1191
Non-polymers61816
Water93752
1
A: Growth/differentiation factor 2
hetero molecules

A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,47434
Polymers24,2382
Non-polymers1,23632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
MethodPISA
Unit cell
Length a, b, c (Å)70.940, 70.940, 145.860
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-507-

CL

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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.: 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.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 1M NaCl, 3.5% PEG8K, 0.3M Citrate pH 3.5

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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: Apr 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→35.47 Å / Num. obs: 10969 / % possible obs: 100 % / Redundancy: 24.6 % / Biso Wilson estimate: 44.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.045 / Rrim(I) all: 0.164 / Χ2: 0.95 / Net I/σ(I): 14
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 20.9 % / Rmerge(I) obs: 2.588 / Mean I/σ(I) obs: 2 / Num. unique obs: 857 / CC1/2: 0.526 / Rpim(I) all: 0.81 / Rrim(I) all: 2.715 / Χ2: 0.98 / % 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: 2.12→35.47 Å / SU ML: 0.304 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.8762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 537 4.9 %
Rwork0.2199 10412 -
obs0.2217 10949 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.21 Å2
Refinement stepCycle: LAST / Resolution: 2.12→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 26 52 904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016868
X-RAY DIFFRACTIONf_angle_d1.55741176
X-RAY DIFFRACTIONf_chiral_restr0.0796128
X-RAY DIFFRACTIONf_plane_restr0.0124147
X-RAY DIFFRACTIONf_dihedral_angle_d13.5576317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.330.27861220.28412544X-RAY DIFFRACTION100
2.33-2.670.31551450.23572548X-RAY DIFFRACTION99.96
2.67-3.360.24121440.21562579X-RAY DIFFRACTION99.85
3.37-35.470.24911260.212741X-RAY DIFFRACTION100
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)
19.811642153121.41051008191-7.411146335939.42977556110.09960527431385.74003296419-0.799134233694-1.07588974233-0.8096536236870.6464858008680.0725115953548-0.7586610031531.374675354422.263163015880.7291445222750.4996833492780.0534129933501-0.0481908941760.819300230419-0.0535346735120.648902760692-4.01158816243-15.5405881867-20.2256913144
26.063629338550.390539969022-0.4667544358345.015470981171.248947707522.01191481076-0.7051138734620.852004258713-0.498691777076-0.922250612620.441631429502-0.4393660501581.042934047621.11394002467-0.06690402221280.725967416414-0.2107993525670.02121498270310.736343450792-0.1143723424210.524408985118-5.04760105896-12.2629380113-34.7642201835
35.49820827303-3.266548296651.611067708064.63035923283-4.309133000018.32957230628-0.530752106522-1.672861824770.1385102365990.0621447127482-0.227628728699-0.813975618728-0.2145407777971.101979749641.022142507330.5071490884190.0833376931126-0.04385588474390.8070875948010.1371738752850.578359488158-12.2446424674-13.1401120327-6.64265100388
47.72195402283-0.965569289889-0.9106518401463.76870627652-2.783491922973.70712868281-0.149101107207-0.210578447478-1.0949622048-0.2426464845790.221983119747-0.5804685713420.736182422661-0.5793553210890.158383191010.5507532332060.0157886334738-0.03818021903420.4960305195140.0981560526040.462696217112-23.5653449216-18.898261359-7.37283745084
52.00269433919-1.49676865399-5.553464105932.102057012243.821376839497.78824464499-0.7644004887130.2943543277191.99813406258-0.3521268003160.62502379516-0.582701823796-1.746604222860.8582296105140.3828798021130.334810163795-0.169515495857-0.1843940573550.4965327613280.02722237853660.421385274588-11.9772297011-8.4457696836-18.0565066099
65.108985320660.960989323193-0.9927270144982.45087013794-0.3281498694842.68845607011-0.07665588232750.7406210626450.597030938237-0.3763973799490.273782215963-0.00257301441729-0.8768729245610.234747376706-0.2154397558040.64341443366-0.143820943203-0.03239088846040.5928168913420.02888199169630.48106458061-7.8194840056-2.49368733084-33.58063584
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 335 )324 - 3351 - 12
22chain 'A' and (resid 336 through 357 )336 - 35713 - 34
33chain 'A' and (resid 358 through 371 )358 - 37135 - 48
44chain 'A' and (resid 372 through 392 )372 - 39249 - 69
55chain 'A' and (resid 393 through 397 )393 - 39770 - 74
66chain 'A' and (resid 398 through 429 )398 - 42975 - 106

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