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- PDB-7poj: Prodomain bound BMP10 crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 7poj
TitleProdomain bound BMP10 crystal form 2
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
Bone morphogenetic protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 1.2Oct 23, 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)92,6187
Polymers91,9814
Non-polymers6373
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-36 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.351, 144.108, 82.129
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-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A321 - 424
221chain 'B'B321 - 424
132(chain 'C' and (resid 80 through 119 or resid 123...C80 - 118
142(chain 'C' and (resid 80 through 119 or resid 123...C123 - 148
152(chain 'C' and (resid 80 through 119 or resid 123...C162 - 170
162(chain 'C' and (resid 80 through 119 or resid 123...C182 - 190
172(chain 'C' and (resid 80 through 119 or resid 123...C195 - 224
182(chain 'C' and (resid 80 through 119 or resid 123...C248 - 260
192(chain 'C' and (resid 80 through 119 or resid 123...C301
2102(chain 'D' and (resid 80 through 225 or resid 248 through 261 or resid 301))D80 - 118
2112(chain 'D' and (resid 80 through 225 or resid 248 through 261 or resid 301))D123 - 148
2122(chain 'D' and (resid 80 through 225 or resid 248 through 261 or resid 301))D162 - 170
2132(chain 'D' and (resid 80 through 225 or resid 248 through 261 or resid 301))D182 - 190
2142(chain 'D' and (resid 80 through 225 or resid 248 through 261 or resid 301))D195 - 224
2152(chain 'D' and (resid 80 through 225 or resid 248 through 261 or resid 301))D248 - 260
2162(chain 'D' and (resid 80 through 225 or resid 248 through 261 or resid 301))D301

NCS ensembles :
ID
1
2

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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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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.: 1 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 20% PEG3350 0.2 M ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 3.5→101.63 Å / Num. obs: 11092 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 152.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.062 / Rrim(I) all: 0.18 / Net I/σ(I): 6.3
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 8.5 % / Rmerge(I) obs: 2.702 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2583 / CC1/2: 0.521 / Rpim(I) all: 0.981 / Rrim(I) all: 2.88 / % possible all: 99.5

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Processing

Software
NameVersionClassification
autoPROCdata processing
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.17_3644refinement
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7POI

7poi


Resolution: 3.5→101.63 Å / SU ML: 0.6979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.5907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2998 531 4.84 %
Rwork0.2746 10448 -
obs0.2758 10978 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 170.01 Å2
Refinement stepCycle: LAST / Resolution: 3.5→101.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 41 1 3942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184032
X-RAY DIFFRACTIONf_angle_d0.48735454
X-RAY DIFFRACTIONf_chiral_restr0.042609
X-RAY DIFFRACTIONf_plane_restr0.0041683
X-RAY DIFFRACTIONf_dihedral_angle_d11.7455538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.850.44461190.38922533X-RAY DIFFRACTION97.57
3.85-4.410.29361290.32212585X-RAY DIFFRACTION99.78
4.41-5.560.29511420.28252604X-RAY DIFFRACTION99.75
5.56-101.630.28391410.24192726X-RAY DIFFRACTION99.65
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)
12.32301016255-2.733082248363.664877029469.16574914833-4.043591919595.70871069360.09031635460280.251308808545-0.240838498706-1.682171071620.165277334461.023709303240.590288029595-1.12453280008-0.2661081124521.382262963220.299365260113-0.1408407475071.76483872030.06239421620791.2265027710867.573696044929.7251479088-2.26430291692
24.81887913485-5.02142788175-4.923717034889.052806771362.34540228366.401842778230.04471411440981.627858601070.133019645423-1.20575765622-0.577029678440.04974998844160.53288393624-0.549840029450.4391001020411.286171166970.137653032821-0.2840231165391.860417285530.03241774414810.9509003841268.267042233146.0184265693-2.40582923367
39.36348278367-3.50315099397-4.619742987377.907280980770.124865074688.93554986571-0.0516956223445-0.3247641933060.2517161662440.158768962426-0.02810319182251.11728876468-0.371659068586-0.4877146925040.1039943766450.7677867396090.0755765710448-0.1680883154281.293270815450.07801388083341.367948954753.406239902768.487415609925.4134823839
49.21512927368-3.851648538581.756910520486.86022855808-0.5893465570624.439242502680.308687305775-0.293339826618-0.355729474593-0.0133488645401-0.454237412947-1.292059369150.1292618855130.09466735163450.1328418190070.8063771617140.142965629895-0.1109123238791.66745392101-0.1275551014641.8627115823190.99573040639.6667802919719.9746294599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 321 through 424)
2X-RAY DIFFRACTION2(chain 'B' and resid 321 through 424)
3X-RAY DIFFRACTION3(chain 'C' and resid 80 through 261)
4X-RAY DIFFRACTION4(chain 'D' and resid 80 through 261)

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