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- PDB-4yci: non-latent pro-bone morphogenetic protein 9 -

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Basic information

Entry
Database: PDB / ID: 4yci
Titlenon-latent pro-bone morphogenetic protein 9
Components(Bone Morphogenetic Protein 9 ...) x 2
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 / positive regulation of BMP signaling pathway / SMAD protein signal transduction / negative regulation of DNA biosynthetic process / signaling receptor activator activity / negative regulation of endothelial cell migration / cartilage development / blood vessel morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of endothelial cell proliferation / negative regulation of DNA replication / positive regulation of Notch signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / 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 / negative regulation of cell growth / neuron differentiation / osteoblast differentiation / glucose metabolic process / positive regulation of angiogenesis / 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 / MOLECULAR REPLACEMENT / Resolution: 3.25 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 1.4Aug 26, 2015Group: Structure summary
Revision 2.0Jul 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 / pdbx_struct_oper_list / struct_asym / struct_conn / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 / _pdbx_struct_oper_list.symmetry_operation / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)91,95516
Polymers90,6564
Non-polymers1,30012
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-224 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.280, 120.280, 221.310
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 AA60 - 3113
211chain BB61 - 3114
112chain CC303 - 407
212chain DD303 - 407

NCS ensembles :
ID
1
2

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Components

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Bone Morphogenetic Protein 9 ... , 2 types, 4 molecules ABCD

#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 / pro-BMP9 growth factor domain / 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

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Sugars , 2 types, 2 molecules

#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.: 1
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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 24 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.1 Å3/Da / Density % sol: 75.9 %
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: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 29711 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.03 % / Biso Wilson estimate: 128.58 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.154 / Χ2: 0.96 / Net I/σ(I): 8.36 / Num. measured all: 119773
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.25-3.330.1233.3940.538800215321473.90599.7
3.33-3.430.1092.4670.738707212921272.84299.9
3.43-3.530.2611.6821.18412206220551.93499.7
3.53-3.630.4011.2371.498115199119851.42499.7
3.63-3.750.5140.8932.028021197019661.0399.8
3.75-3.880.7430.612.877688188818840.70299.8
3.88-4.030.8660.4114.147335181718150.47399.9
4.03-4.20.9230.285.597134173817360.32299.9
4.2-4.380.950.2037.536812168116780.23499.8
4.38-4.60.9810.1369.66596163016280.15799.9
4.6-4.840.9880.10811.786239154915470.12499.9
4.84-5.140.9890.09512.925862144914440.1199.7
5.14-5.490.9930.08813.395547139613940.10299.9
5.49-5.930.9890.09213.735127128112740.10699.5
5.93-6.50.9920.07915.284725119611870.09199.2
6.5-7.270.9940.0619.34238108310710.0798.9
7.27-8.390.9970.04423.5437679759600.05198.5
8.39-10.280.9960.03827.2630888268100.04498.1
10.28-14.530.9970.03628.7923496586380.04297
14.53-500.9940.04229.1112114023650.05190.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YCG

4ycg


Resolution: 3.25→48.863 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1500 5.1 %thin shell random selection
Rwork0.2396 27899 --
obs0.2406 29399 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 460.92 Å2 / Biso mean: 147.7245 Å2 / Biso min: 56.04 Å2
Refinement stepCycle: final / Resolution: 3.25→48.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 66 0 4747
Biso mean--186.32 --
Num. residues----591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224893
X-RAY DIFFRACTIONf_angle_d0.6166587
X-RAY DIFFRACTIONf_chiral_restr0.032747
X-RAY DIFFRACTIONf_plane_restr0.003843
X-RAY DIFFRACTIONf_dihedral_angle_d9.6731799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1688X-RAY DIFFRACTION5.561TORSIONAL
12B1688X-RAY DIFFRACTION5.561TORSIONAL
21C982X-RAY DIFFRACTION5.561TORSIONAL
22D982X-RAY DIFFRACTION5.561TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2501-3.35490.3841500.38732248239890
3.3549-3.47480.4178810.35552521260298
3.4748-3.61390.37471610.33042495265699
3.6139-3.77830.31621650.301525092674100
3.7783-3.97740.3121790.259726022681100
3.9774-4.22650.25951590.229625292688100
4.2265-4.55260.22441590.190125522711100
4.5526-5.01040.18481470.17925602707100
5.0104-5.73440.2485930.21626392732100
5.7344-7.2210.27381580.26732570272899
7.221-48.86810.24441480.23112674282297
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)
16.5286-1.4372-2.15314.3070.47466.34880.19440.2186-0.11440.1495-0.4523-0.24240.2940.08340.29261.3159-0.18050.29890.80310.01010.7443.059185.1844490.7673
24.81651.7262-1.56976.7174-1.2853.74760.49880.25870.38930.5717-0.0556-0.3532-0.6103-0.2478-0.41811.46660.4678-0.21180.81070.11111.007190.709335.1264447.76
33.1397-3.5268-3.75834.65933.09426.7352-0.0466-0.35840.17950.0632-0.123-0.2353-0.26551.01550.16750.67970.02910.01581.00980.16330.626365.44186.29457.9113
42.2525-2.146-0.73566.25342.69775.01640.29880.3023-0.5454-1.2983-0.41970.45920.38760.24960.05861.02360.2460.01160.88640.26921.172567.743268.1999442.0013
55.80242.89437.591.47473.77879.82842.12142.8757-0.3232.87483.39493.5599-2.77421.4306-3.31432.73440.99161.27943.02041.4162.686779.897364.6341449.6469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and ((resseq 80:244))B80 - 244
2X-RAY DIFFRACTION2chain 'A' and ((resseq 80:238))A80 - 238
3X-RAY DIFFRACTION3(chain 'B' and resseq 61:79) or (chain 'D' and resseq 303:407)B61 - 79
4X-RAY DIFFRACTION3(chain 'B' and resseq 61:79) or (chain 'D' and resseq 303:407)D303 - 407
5X-RAY DIFFRACTION4(chain 'A' and resseq 61:79) or (chain 'C' and resseq 303:407)A61 - 79
6X-RAY DIFFRACTION4(chain 'A' and resseq 61:79) or (chain 'C' and resseq 303:407)C303 - 407
7X-RAY DIFFRACTION5chain 'A' and ((resseq 239:258))A0

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