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- PDB-7poi: Prodomain bound BMP10 crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 7poi
TitleProdomain bound BMP10 crystal form 1
Components(Bone morphogenetic protein 10) x 2
KeywordsCYTOKINE / BMP10 bone morphogenetic protein prodomain TGFbeta signalling
Function / homology
Function and homology information


regulation of cardiac muscle hypertrophy in response to stress / positive regulation of sarcomere organization / positive regulation of cell proliferation involved in heart morphogenesis / atrial cardiac muscle tissue morphogenesis / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway ...regulation of cardiac muscle hypertrophy in response to stress / positive regulation of sarcomere organization / positive regulation of cell proliferation involved in heart morphogenesis / atrial cardiac muscle tissue morphogenesis / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway / receptor serine/threonine kinase binding / adult heart development / heart trabecula formation / negative regulation of endothelial cell migration / sarcomere organization / Molecules associated with elastic fibres / ventricular cardiac muscle tissue morphogenesis / positive regulation of cardiac muscle hypertrophy / positive regulation of SMAD protein signal transduction / cardiac muscle cell proliferation / regulation of cardiac muscle contraction / BMP signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of cell migration / cytokine activity / growth factor activity / kidney development / negative regulation of cell growth / hormone activity / Z disc / cell adhesion / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular region / cytoplasm
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
D(-)-TARTARIC ACID / Bone morphogenetic protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGuo, J. / Yu, M. / Li, W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/12/54/29734, PG/17/1/32532, FS/SBSRF/20/31005 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10.
Authors: Guo, J. / Liu, B. / Thorikay, M. / Yu, M. / Li, X. / Tong, Z. / Salmon, R.M. / Read, R.J. / Ten Dijke, P. / Morrell, N.W. / Li, W.
History
DepositionSep 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein 10
B: Bone morphogenetic protein 10
C: Bone morphogenetic protein 10
D: Bone morphogenetic protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5747
Polymers91,9814
Non-polymers5933
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.897, 214.041, 106.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2(chain "C" and (resid 81 through 117 or resid 126 through 172 or resid 181 through 301))
d_2ens_2(chain "D" and (resid 81 through 148 or resid 162 through 260 or resid 301))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNARGA1 - 104
d_21ens_1ASNARGB1 - 104
d_11ens_2PROPROC3 - 39
d_12ens_2TYRGLUC48 - 81
d_13ens_2ARGGLNC84 - 143
d_14ens_2NAGNAGD
d_21ens_2PROTYRE1 - 60
d_22ens_2ASPGLNE63 - 133
d_23ens_2NAGNAGF

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.53269060942, 0.00318576476634, 0.846304062107), (0.00226507900262, -0.999983966641, 0.00518997863626), (0.846307027061, 0.00468159844354, 0.532674852592)-22.8123402897, -44.5767211435, 12.7779660165
2given(-0.547770919491, -0.00606310654876, 0.83660639401), (0.0569261657489, -0.997926343931, 0.0300403685464), (0.834689422128, 0.0640800345525, 0.546980180408)-23.0261030136, -44.9111217018, 15.4161478942

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Components

#1: Protein Bone morphogenetic protein 10 / BMP-10


Mass: 12177.185 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Cell line (production host): HEK EBNA / Production host: Homo sapiens (human) / References: UniProt: O95393
#2: Protein Bone morphogenetic protein 10 / BMP-10


Mass: 33813.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Cell line (production host): HEK EBNA / Production host: Homo sapiens (human) / References: UniProt: O95393
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 19% PEG 3350 0.15 M Ammonium tartrate dibasic 0.02 M Sodium cacodylate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.9→107.02 Å / Num. obs: 19024 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 91.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.048 / Rrim(I) all: 0.173 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 12.8 % / Rmerge(I) obs: 3.761 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3033 / CC1/2: 0.482 / Rpim(I) all: 1.094 / Rrim(I) all: 3.919 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALS1.14.5data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SF3, 4YCI

6sf3

4yci


Resolution: 2.9→107.02 Å / SU ML: 0.5248 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 34.0263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2684 968 5.1 %
Rwork0.2185 33990 -
obs0.2209 18998 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 112.09 Å2
Refinement stepCycle: LAST / Resolution: 2.9→107.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 38 11 3978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224060
X-RAY DIFFRACTIONf_angle_d0.47015497
X-RAY DIFFRACTIONf_chiral_restr0.0433611
X-RAY DIFFRACTIONf_plane_restr0.004693
X-RAY DIFFRACTIONf_dihedral_angle_d14.94621508
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.542279018527
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.65146226248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.40541020.38122674X-RAY DIFFRACTION99.82
2.98-3.070.40881520.36542616X-RAY DIFFRACTION99.64
3.07-3.170.4341370.34682614X-RAY DIFFRACTION99.78
3.17-3.280.34571340.29212572X-RAY DIFFRACTION99.85
3.28-3.410.33511450.27862635X-RAY DIFFRACTION99.89
3.41-3.560.33071350.25212593X-RAY DIFFRACTION99.78
3.56-3.750.25351330.24582624X-RAY DIFFRACTION99.89
3.75-3.990.2431610.2232614X-RAY DIFFRACTION99.93
3.99-4.30.25711420.19292608X-RAY DIFFRACTION100
4.3-4.730.24421300.16332629X-RAY DIFFRACTION100
4.73-5.410.22371840.18022575X-RAY DIFFRACTION100
5.41-6.820.30451390.22072624X-RAY DIFFRACTION100
6.82-107.020.22671330.1942612X-RAY DIFFRACTION99.35
Refinement TLS params.Method: refined / Origin x: -3.41330751624 Å / Origin y: -22.6833408638 Å / Origin z: 19.663638474 Å
111213212223313233
T0.655657993381 Å2-0.198930489185 Å20.0836183497324 Å2-0.852948447634 Å2-0.0176319589254 Å2--0.282100839355 Å2
L1.59637506289 °2-1.0033141669 °20.481405644894 °2-2.68730779016 °2-0.01366447971 °2--1.19896380519 °2
S0.144186284875 Å °0.0437807030335 Å °-0.0430720823357 Å °-0.167418253086 Å °-0.14072786243 Å °0.164620085901 Å °-0.283708133718 Å °-0.0483472096635 Å °0.0354416130738 Å °
Refinement TLS groupSelection details: all

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