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- PDB-4n1d: Nodal/BMP2 chimera NB250 -

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Basic information

Entry
Database: PDB / ID: 4n1d
TitleNodal/BMP2 chimera NB250
ComponentsNodal/BMP2 chimera protein
KeywordsCytokine / Signaling Protein
Function / homology
Function and homology information


floor plate morphogenesis / left lung morphogenesis / epiblast cell-extraembryonic ectoderm cell signaling / negative regulation of chorionic trophoblast cell proliferation / negative regulation of cell development / type I activin receptor binding / polarity specification of proximal/distal axis / neural fold formation / axial mesodermal cell fate specification / embryonic process involved in female pregnancy ...floor plate morphogenesis / left lung morphogenesis / epiblast cell-extraembryonic ectoderm cell signaling / negative regulation of chorionic trophoblast cell proliferation / negative regulation of cell development / type I activin receptor binding / polarity specification of proximal/distal axis / neural fold formation / axial mesodermal cell fate specification / embryonic process involved in female pregnancy / Regulation of signaling by NODAL / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification / mesendoderm development / nodal signaling pathway / positive regulation of extracellular matrix constituent secretion / morphogen activity / enzyme activator complex / regulation of gastrulation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / negative regulation of cardiac muscle cell differentiation / corticotropin hormone secreting cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / formation of anatomical boundary / thyroid-stimulating hormone-secreting cell differentiation / trophectodermal cellular morphogenesis / inhibition of neuroepithelial cell differentiation / positive regulation of phosphatase activity / cell migration involved in gastrulation / maternal process involved in parturition / mesenchyme development / ameloblast differentiation / aortic valve development / telencephalon regionalization / primitive streak formation / regulation of stem cell population maintenance / maternal placenta development / negative regulation of trophoblast cell migration / heart induction / positive regulation of odontogenesis / positive regulation of cartilage development / determination of left/right asymmetry in lateral mesoderm / positive regulation of peroxisome proliferator activated receptor signaling pathway / lung vasculature development / pericardium development / BMP receptor complex / positive regulation of cell-cell adhesion / proteoglycan metabolic process / co-receptor binding / negative regulation of androgen receptor signaling pathway / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / telencephalon development / positive regulation of odontoblast differentiation / positive regulation of bone mineralization involved in bone maturation / endocardial cushion formation / Transcriptional regulation by RUNX2 / phosphatase activator activity / positive regulation of astrocyte differentiation / cellular response to BMP stimulus / cardiac muscle cell differentiation / Signaling by BMP / embryonic pattern specification / astrocyte differentiation / Signaling by NODAL / vasculature development / embryonic cranial skeleton morphogenesis / positive regulation of ossification / cardiac muscle tissue morphogenesis / positive regulation of p38MAPK cascade / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / Molecules associated with elastic fibres / branching involved in ureteric bud morphogenesis / digestive tract morphogenesis / negative regulation of fat cell differentiation / bone mineralization / positive regulation of osteoblast proliferation / endodermal cell differentiation / heart looping / odontogenesis of dentin-containing tooth / germ cell development / : / inner ear development / negative regulation of cell cycle / somatic stem cell population maintenance / positive regulation of SMAD protein signal transduction / positive regulation of vascular endothelial growth factor production / positive regulation of Wnt signaling pathway / cell fate commitment
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. ...: / 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
Bone morphogenetic protein 2 / Nodal homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.912 Å
AuthorsEsquivies, L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Designer Nodal/BMP2 Chimeras Mimic Nodal Signaling, Promote Chondrogenesis, and Reveal a BMP2-like Structure.
Authors: Esquivies, L. / Blackler, A. / Peran, M. / Rodriguez-Esteban, C. / Izpisua Belmonte, J.C. / Booker, E. / Gray, P.C. / Ahn, C. / Kwiatkowski, W. / Choe, S.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nodal/BMP2 chimera protein


Theoretical massNumber of molelcules
Total (without water)13,5851
Polymers13,5851
Non-polymers00
Water1,29772
1
A: Nodal/BMP2 chimera protein

A: Nodal/BMP2 chimera protein


Theoretical massNumber of molelcules
Total (without water)27,1692
Polymers27,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2970 Å2
ΔGint-28 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.570, 95.570, 97.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-252-

HOH

21A-267-

HOH

DetailsDimer generated by the operations: y,x,-z

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Components

#1: Protein Nodal/BMP2 chimera protein / BMP-2 / Bone morphogenetic protein 2A / BMP-2A


Mass: 13584.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A, Nodal / Production host: Escherichia coli (E. coli) / References: UniProt: P12643, UniProt: Q96S42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M NaCl, 0.1 M Na acetate pH 4.6, 30% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2012
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.912→31.548 Å / Num. obs: 13316 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rsym value: 0.033 / Net I/σ(I): 41.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.91-2.027.40.3422.31350118210.34294.3
2.02-2.1410.30.2373.31895118450.237100
2.14-2.29100.1574.91722117220.157100
2.29-2.4710.20.17.71626616010.1100
2.47-2.710.20.06711.31515814890.067100
2.7-3.029.90.04317.11344313520.043100
3.02-3.4910.20.02726.31215611930.027100
3.49-4.289.90.01738.41031010400.017100
4.28-6.059.70.01542.176377870.015100
6.05-31.5489.20.01540.942824660.01599.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.912→31.548 Å / Occupancy max: 1 / Occupancy min: 0.7 / SU ML: 0.16 / σ(F): 1.36 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1328 9.97 %random
Rwork0.1754 ---
obs0.1784 13314 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.87 Å2 / Biso mean: 43.1648 Å2 / Biso min: 24.52 Å2
Refinement stepCycle: LAST / Resolution: 1.912→31.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 0 72 924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006881
X-RAY DIFFRACTIONf_angle_d1.1361192
X-RAY DIFFRACTIONf_chiral_restr0.08123
X-RAY DIFFRACTIONf_plane_restr0.004155
X-RAY DIFFRACTIONf_dihedral_angle_d13.981329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.912-1.98850.2261370.19091226136392
1.9885-2.0790.211530.180813291482100
2.079-2.18860.21471610.181312931454100
2.1886-2.32570.21991370.171613441481100
2.3257-2.50520.20521270.18113571484100
2.5052-2.75720.2421480.178813431491100
2.7572-3.15580.20291540.17513351489100
3.1558-3.97480.17821460.164213641510100
3.9748-31.55220.20581650.178813951560100
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)
16.4131-4.48131.31553.45370.11414.2830.70371.26651.1698-0.663-0.6546-0.7249-0.5758-0.26250.0440.49760.02810.15570.36760.13260.401-8.2518-22.7055-13.4475
28.7415-0.58230.38723.94290.95592.68610.292-0.4140.38670.3280.0967-1.1056-0.09970.7709-0.32070.3115-0.03180.04930.3541-0.07310.41745.8878-38.0431-9.8317
38.6917-8.8799-6.19099.39065.86676.18940.2858-0.03950.8487-0.38270.1717-0.6417-0.54280.063-0.4520.3760.00610.07590.2970.01490.3232-5.5108-28.055-12.5681
46.2733-4.2641-2.83348.20667.50588.32420.65460.17990.5821-0.55150.0002-0.2044-1.28290.0912-0.71650.56120.11830.16010.35250.05050.486-20.1226-13.6401-4.7348
59.55457.4252-6.97185.7572-5.3945.1323-0.08941.26680.8054-1.43760.13720.5811-0.0552-1.0843-0.12450.58340.0943-0.030.5770.02130.3495-24.3682-20.8025-6.6805
66.3158-1.3734-3.62263.9795-2.26878.15450.71840.21321.4934-0.0625-0.068-0.1724-1.33630.2927-0.59230.4579-0.00280.15340.3338-0.02860.4491-22.3346-12.17764.463
78.1125-5.7805-6.66644.29114.83045.6324-0.04450.3138-0.1553-0.530.0888-0.1007-0.2821-0.18530.10660.31280.0513-0.00960.37430.00340.2422-15.2063-25.3933-4.9201
89.8005-6.68380.43466.07670.23430.5460.2320.0459-0.1754-0.1087-0.0209-0.04140.13210.0797-0.17050.30780.00620.0260.2848-0.03530.2897-3.0915-42.2527-9.4209
94.8392-5.0982.95275.552-2.76929.1305-0.1045-0.4659-0.0460.61320.08820.02930.22650.1845-0.04640.3326-0.0227-0.00070.3186-0.03720.33212.3743-48.6655-5.2054
103.1273-4.9767-1.48488.40293.19482.23670.12960.0951-0.2306-0.0409-0.16290.4684-0.0692-0.34140.02160.2953-0.00380.04340.31870.00250.2268-13.5036-30.2317-6.9732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 36 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 44 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 52 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 58 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 78 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 84 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 85 through 93 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 94 through 104 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 105 through 115 )A0

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