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- PDB-9dpv: BMP-9 K357R G389S Dimer Without Radiation Damage in Neutral pH -

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Basic information

Entry
Database: PDB / ID: 9dpv
TitleBMP-9 K357R G389S Dimer Without 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: 1.99 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)12,53811
Polymers12,1771
Non-polymers36110
Water1,56787
1
A: Growth/differentiation factor 2
hetero molecules

A: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,07722
Polymers24,3542
Non-polymers72320
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)71.105, 71.105, 145.553
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-504-

CL

21A-621-

HOH

31A-656-

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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.78 Å3/Da / Density % sol: 67.44 %
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: 1.99→41.37 Å / Num. obs: 13055 / % possible obs: 98.8 % / Redundancy: 7 % / Biso Wilson estimate: 36.87 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.081 / Rrim(I) all: 0.168 / Χ2: 1 / Net I/σ(I): 6.4
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 832 / CC1/2: 0.645 / Rpim(I) all: 0.877 / Rrim(I) all: 1.723 / Χ2: 0.95 / % possible all: 86.7
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: 1.99→35.55 Å / SU ML: 0.248 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 28.1713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2649 649 4.99 %
Rwork0.2238 12348 -
obs0.2259 12997 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.46 Å2
Refinement stepCycle: LAST / Resolution: 1.99→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 15 87 928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094854
X-RAY DIFFRACTIONf_angle_d1.24781158
X-RAY DIFFRACTIONf_chiral_restr0.0653127
X-RAY DIFFRACTIONf_plane_restr0.0143145
X-RAY DIFFRACTIONf_dihedral_angle_d12.0951312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.140.32031220.30312313X-RAY DIFFRACTION94.02
2.14-2.360.25891360.23112441X-RAY DIFFRACTION99.38
2.36-2.70.24421230.23282474X-RAY DIFFRACTION99.16
2.7-3.40.2491250.19572507X-RAY DIFFRACTION99.51
3.41-35.550.27071430.2242613X-RAY DIFFRACTION99.21
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)
14.464118514730.5554003426772.358241479396.835538233754.136818961523.461533390410.5428734564490.0974408182245-0.6894815715330.682054256171-0.6294592874130.3128640746341.08238858485-1.122179222790.2968945702590.559353072358-0.000455770105152-0.03343858007310.425135817360.02191640760990.339508351320.29105704844.0561823395315.3896947138
21.81245487457-0.362041608940.7407071431143.693440328231.618396521562.637500950920.6511246362660.909889864666-0.336829195217-0.659575184989-0.6936060876370.4774440623940.204181732278-0.544178084197-0.07659532733680.6512591973140.309262115294-0.1376358001460.726527684558-0.03110966210950.25034916436423.20665087185.260828198661.6958395929
37.190680996574.82363331231-3.704732028155.038009806640.1361454259177.10296763069-0.617573333110.277005276924-1.367304156840.844047073091-0.161416168774-0.4554096837221.63170937135-0.04816921621870.5873887519830.767941397548-0.08054533366730.1350642183990.365162232824-0.002904573397910.41200973037122.527388464112.202935101429.841701487
42.235978324920.138918662442-2.093172205674.32015112436-0.1158329775924.970880070460.2228341692220.290712370193-0.1742845198270.18241636987-0.2507776076520.373800739522-0.0249529786204-0.3637965041120.0850600202320.406321368008-0.09029113164120.03178301048690.4168517760370.02750254906130.22536320695216.787827762623.7257135928.6515954363
53.64266322366-0.5775420485310.04176338868454.144541052182.055045890981.962269718370.3292756759470.9516571225240.147974029361-0.420273162075-0.0234203082548-0.4805011422410.4009195661040.569814567219-0.297465305410.4207163482820.2273349969150.04712216028650.6325473878360.08323854732970.2669364324132.09089383368.485566910921.15566158278
64.27480277861-1.55567358875-3.196984707134.433891527123.32213880976.179235288380.3861797050.429292567203-0.0132680585282-0.107526524398-0.277491446036-0.5878612479820.1253554910690.216955768234-0.0643900832950.3821166691250.144716581622-0.0206796036050.4128431170740.07677089688690.27466405302732.35785956558.243366470258.3170819313
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 325 through 335 )325 - 3351 - 11
22chain 'A' and (resid 336 through 357 )336 - 35712 - 33
33chain 'A' and (resid 358 through 371 )358 - 37134 - 47
44chain 'A' and (resid 372 through 392 )372 - 39248 - 68
55chain 'A' and (resid 393 through 411 )393 - 41169 - 87
66chain 'A' and (resid 412 through 429 )412 - 42988 - 105

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