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- PDB-9dpm: BMP-9 Monomer Growth Factor with Cysteinylation -

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Basic information

Entry
Database: PDB / ID: 9dpm
TitleBMP-9 Monomer Growth Factor with Cysteinylation
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
CYSTEINE / Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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)12,4158
Polymers12,1191
Non-polymers2967
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC-MALS shows monomer form is monomeric at biologically relevant concentrations.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.863, 71.863, 144.606
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-687-

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-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.9 M sodium chloride, 133 mM HEPES, 166 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 15387 / % possible obs: 100 % / Redundancy: 23.78 % / Biso Wilson estimate: 40.09 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.028 / Rrim(I) all: 0.139 / Χ2: 0.687 / Net I/av σ(I): 24.625 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 3.025 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 962 / CC1/2: 0.598 / CC star: 0.865 / Rpim(I) all: 0.643 / Rrim(I) all: 3.093 / Χ2: 0.544 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.46 Å / SU ML: 0.3435 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.4101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2417 740 4.82 %
Rwork0.2046 14599 -
obs0.2064 15339 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 13 88 927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046866
X-RAY DIFFRACTIONf_angle_d0.77031176
X-RAY DIFFRACTIONf_chiral_restr0.0454129
X-RAY DIFFRACTIONf_plane_restr0.0043148
X-RAY DIFFRACTIONf_dihedral_angle_d11.7633320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.40271200.35842869X-RAY DIFFRACTION99.43
2.05-2.250.30551690.28292835X-RAY DIFFRACTION99.47
2.25-2.580.30451550.23612889X-RAY DIFFRACTION99.97
2.58-3.250.25671480.212923X-RAY DIFFRACTION99.97
3.25-29.460.20011480.1733083X-RAY DIFFRACTION99.81
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)
16.204627229291.692143231697.606784205689.216403405155.369852208142.001238881250.45517255968-2.19458772431-0.9368716100412.03442991409-0.5004297398220.5431008462520.563018542238-1.814802701721.375431128580.894742376569-0.0847129521058-0.05472044404280.6415734719280.2752486565630.39094568163820.0185.53922.986
23.69259158837-0.0262892876253-0.608764704372.042356867281.798719316743.834513298960.4210787265641.69547406493-0.335671606064-0.957246618591-0.7393183816840.4102917810090.359409554021-0.05597687131590.329841187120.7299117015110.27015492885-0.09432149543970.801399217495-0.04999049605430.41954084144523.1064.963-1.597
34.59239307207-2.66225042871-4.440491828714.853576195523.248525029594.56606100582-0.210044800255-0.0515990539455-0.2204932487960.959805694718-0.5601332609160.7466387448880.798228561008-0.04001143339150.3207597916090.770070320455-0.01377338384930.04287752271770.5398689092620.0236279284120.43036090721520.957.88919.211
43.24851098235-2.5590409521-1.252308364176.365286192311.031652410846.9019347443-0.0168833628056-0.225434045092-0.8832248173560.441213345706-0.003804187011430.1478540800940.6373713827890.0997705746315-0.1407494895540.671287056161-0.135553205128-0.03892390659690.5198916657610.06117363253890.36040620517622.00419.9229.854
52.39249747423-1.28573342006-0.2601986074283.14992695054-3.020355690356.966502389390.7815277730480.3566536965440.132886913952-1.08807826137-0.277883343540.390640521546-0.0362960256244-0.635831537882-0.1207487983970.427511280827-0.0974974491453-0.01869809986640.5272630331160.03196008460190.39071719320413.38724.46425.648
67.219526426322.90901976481-5.530284225554.470898345050.07256709175746.067734368710.804373450764-0.3025474340620.06963594969330.297836263143-0.218451218154-0.2223520459950.08336509260270.339590003573-0.3219983388350.6473202290020.0437367223038-0.01729436670080.4459656612430.02594908625230.37042421510926.92312.43818.18
73.724814828691.87658732496-0.4093164894075.041239846261.597189719490.842296457233-0.2225459651641.206271522510.316855868955-1.269840966870.142646497774-0.0106879493859-0.2872578461180.904445717642-0.5644416810450.8856920644210.2404271454040.04324002601260.9223045698140.09510373051890.39642426642834.2267.099-4.872
83.74603050792-1.37604378609-2.074780667554.847489168310.8127032774054.488992176670.1745958415150.214714852643-0.158687881376-0.111428140106-0.25515139778-0.3885545809770.3623247742220.1703863744610.01052330215080.4980437863780.130778370469-0.01533331762930.5456106706530.05828191562710.38003593495632.4378.3078.277
92.90115917785-0.212685729831.819489355055.99907692502-6.820718619758.61492218908-1.05124003308-0.330836642288-0.6264688167410.4109174457672.048001515341.13908178031-0.00341890211051-2.7450295616-1.743677807910.879808240517-0.0451973084193-0.01371379878360.62057308463-0.01103939521490.46780413345616.7620.6717.912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 324:330 )A324 - 330
2X-RAY DIFFRACTION2( CHAIN A AND RESID 331:349 )A331 - 349
3X-RAY DIFFRACTION3( CHAIN A AND RESID 350:365 )A350 - 365
4X-RAY DIFFRACTION4( CHAIN A AND RESID 366:383 )A366 - 383
5X-RAY DIFFRACTION5( CHAIN A AND RESID 384:392 )A384 - 392
6X-RAY DIFFRACTION6( CHAIN A AND RESID 393:397 )A393 - 397
7X-RAY DIFFRACTION7( CHAIN A AND RESID 398:411 )A398 - 411
8X-RAY DIFFRACTION8( CHAIN A AND RESID 412:429 )A412 - 429
9X-RAY DIFFRACTION9( CHAIN A AND RESID 501:501 )A501

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