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- PDB-4ycg: Pro-bone morphogenetic protein 9 -

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Basic information

Entry
Database: PDB / ID: 4ycg
TitlePro-bone morphogenetic protein 9
Components
  • Bone Morphogenetic Protein 9 Growth Factor Domain
  • Bone Morphogenetic Protein 9 Prodomain
KeywordsCYTOKINE / pro-BMP complex / morphogen / transforming growth factor-beta family
Function / homology
Function and homology information


: / : / Signaling by BMP / positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / BMP receptor binding / positive regulation of bicellular tight junction assembly / Signaling by BMP / cellular response to BMP stimulus ...: / : / Signaling by BMP / positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / BMP receptor binding / positive regulation of bicellular tight junction assembly / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / SMAD protein signal transduction / positive regulation of BMP signaling pathway / negative regulation of DNA biosynthetic process / signaling receptor activator activity / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / branching involved in blood vessel morphogenesis / negative regulation of DNA replication / positive regulation of Notch signaling pathway / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / vasculogenesis / BMP signaling pathway / positive regulation of endothelial cell proliferation / protein serine/threonine kinase activator activity / ossification / negative regulation of angiogenesis / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / neuron differentiation / negative regulation of cell growth / osteoblast differentiation / positive regulation of angiogenesis / glucose metabolic process / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / 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 Cytokines, subunit B ...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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Growth/differentiation factor 2 / Growth/differentiation factor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.3 Å
AuthorsMi, L.-Z. / Brown, C.T. / Gao, Y. / Tian, Y. / Le, V. / Walz, T. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of bone morphogenetic protein 9 procomplex.
Authors: Mi, L.Z. / Brown, C.T. / Gao, Y. / Tian, Y. / Le, V.Q. / Walz, T. / Springer, T.A.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Structure summary
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Apr 1, 2015Group: Database references
Revision 2.0Nov 1, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _citation.journal_id_CSD ..._atom_site.label_asym_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone Morphogenetic Protein 9 Growth Factor Domain
B: Bone Morphogenetic Protein 9 Growth Factor Domain
C: Bone Morphogenetic Protein 9 Prodomain
D: Bone Morphogenetic Protein 9 Prodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,15816
Polymers90,6564
Non-polymers1,50312
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-59 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.780, 120.780, 220.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA62 - 3114
211chain BB61 - 3114
112chain CC302 - 407
212chain DD302 - 407

NCS ensembles :
ID
1
2
DetailsAssembly confirmed by gel-filtration, ITC, SDS-PAGE

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Components

#1: Protein Bone Morphogenetic Protein 9 Growth Factor Domain / pro-BMP9 prodomain / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 33224.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gdf2, Bmp9 / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9WV56
#2: Protein Bone Morphogenetic Protein 9 Prodomain / BMP9 growth factor / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12102.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9UK05
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 5.12 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.15 M zinc acetate, 0.1 M sodium cacodylate pH 5.8, 4% isopropanol, 0.15 M nondetergent sulfobetaine (NDSB-211)
PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2823,0.97918
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28231
20.979181
ReflectionNumber: 456493 / Rmerge(I) obs: 0.19 / Χ2: 1.52 / D res high: 3.6 Å / Num. obs: 43024 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
16.15046710.03
11.3816.188510.038
9.311.38112210.045
8.059.3137310.058
7.28.05152210.086
6.577.2169710.125
6.096.57182610.159
5.696.09199710.2
5.375.69210510.201
5.095.37219810.235
4.855.09237010.249
4.654.85244210.286
4.474.65254010.385
4.34.47265510.56
4.164.3274410.819
4.034.16289311.167
3.94.03290811.636
3.793.9297512.376
3.693.79311413.362
3.63.69319114.821
ReflectionResolution: 3.3→50 Å / Num. obs: 54034 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 23.3 % / Biso Wilson estimate: 142.69 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.264 / Rrim(I) all: 0.276 / Χ2: 0.806 / Net I/σ(I): 7.58 / Num. measured all: 664651
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.3-3.3923.90.1184.5530.5549515398739874.749100
3.39-3.480.2123.2320.7848594390439043.371100
3.48-3.580.3822.321.1647317381438132.421100
3.58-3.690.521.6881.5946148371037071.76299.9
3.69-3.810.6821.332.1544440358335811.38899.9
3.81-3.940.7880.9593.0142441342634231.00199.9
3.94-4.090.8580.7364.0141053331433110.76899.9
4.09-4.260.9270.5545.4240489328332800.57999.9
4.26-4.450.960.4127.5537481304830430.4399.8
4.45-4.670.9780.3389.1136162294429380.35399.8
4.67-4.920.980.28810.8534191280027930.30199.8
4.92-5.220.9610.27411.1132274264526410.28699.8
5.22-5.580.9820.24512.3930096245724490.25699.7
5.58-6.030.9850.25612.6128951235023430.26799.7
6.03-6.60.9880.2214.6325980213521270.2399.6
6.6-7.380.9920.18717.5223168192919190.19699.5
7.38-8.520.9960.14320.6219587167716680.1599.5
8.52-10.440.9970.1323.6817274144314340.13599.4
10.44-14.760.9980.10825.513199110810950.11298.8
14.76-500.9940.10625.1562916075780.11195.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SOLVE2.15phasing
RESOLVE2.15phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 3.3→48.788 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2739 5.08 %thin shell random selection
Rwork0.2129 51214 --
obs0.2138 53953 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 352.03 Å2 / Biso mean: 172.4435 Å2 / Biso min: 75.83 Å2
Refinement stepCycle: final / Resolution: 3.3→48.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4802 0 86 1 4889
Biso mean--204.71 346.99 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024978
X-RAY DIFFRACTIONf_angle_d0.5886753
X-RAY DIFFRACTIONf_chiral_restr0.023768
X-RAY DIFFRACTIONf_plane_restr0.003865
X-RAY DIFFRACTIONf_dihedral_angle_d10.2881824
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1828X-RAY DIFFRACTION0.458TORSIONAL
12B1828X-RAY DIFFRACTION0.458TORSIONAL
21C986X-RAY DIFFRACTION0.458TORSIONAL
22D986X-RAY DIFFRACTION0.458TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.35690.31441420.33522550269298
3.3569-3.4180.37221480.33224942642100
3.418-3.48370.3031440.326825902734100
3.4837-3.55480.3711500.33825812731100
3.5548-3.6320.3411380.325725362674100
3.632-3.71650.3382160.299826412657100
3.7165-3.80940.32481520.269926092761100
3.8094-3.91240.29151540.256325142668100
3.9124-4.02740.25131420.227726092751100
4.0274-4.15740.20161540.204325292683100
4.1574-4.30590.25111420.193325382680100
4.3059-4.47820.21551480.169225952743100
4.4782-4.68180.16751500.161125332683100
4.6818-4.92840.16581460.155925322678100
4.9284-5.23690.22361440.171826272771100
5.2369-5.64070.19971400.183525062646100
5.6407-6.20730.22781340.214525502684100
6.2073-7.10320.2511320.21625812713100
7.1032-8.94020.20651350.19982540267599
8.9402-48.79310.21671280.22262559268799
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)
12.7248-2.291-2.47555.80132.7146.42220.1405-0.36510.3838-0.1335-0.0317-0.4616-0.74860.7383-0.02950.80220.0364-0.02021.13340.18340.93655.2737-17.5689235.5384
23.2299-4.0497-0.77437.75214.32154.72040.93680.6972-0.8267-1.6826-1.01410.81330.3848-0.23970.10781.40260.2979-0.02470.96420.19311.4597.9243-35.1355220.3582
34.9183-0.142-1.12015.9295-2.97574.81960.2780.42460.0893-0.3198-0.0588-0.26790.1305-0.2106-0.23011.60040.4273-0.16041.05530.07171.111930.6824-68.8644225.9838
47.7572-1.3582-0.88216.8302-3.01218.140.10730.27650.17170.3299-0.8675-0.47060.50920.15140.62271.2354-0.13580.26650.93710.06620.992-17.523-18.6067269.1936
58.37033.548-1.13684.0449-3.84725.22141.90482.4460.63150.7711.23311.78091.3646-0.4408-2.81042.20930.7540.20392.36630.68022.049420.5349-38.3139227.5178
63.9026-0.27494.6453.6851-1.21615.7446-0.75981.07920.9533-0.0826-2.7032-1.22440.65130.63623.29552.20160.42080.34863.35350.8492.4133-7.651-23.524239.0799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resseq 61: 77) or chain 'D'B0
2X-RAY DIFFRACTION2(chain 'A' and resseq 61: 77) or chain 'C'A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 78:238))A78 - 238
4X-RAY DIFFRACTION4chain 'B' and ((resseq 78:238))B78 - 238
5X-RAY DIFFRACTION5chain 'A' and ((resseq 239:258))A0
6X-RAY DIFFRACTION6chain 'B' and ((resseq 239:258))B0

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