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- PDB-4mid: Crystal Structure of Activin A/BMP2 chimera -

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Basic information

Entry
Database: PDB / ID: 4mid
TitleCrystal Structure of Activin A/BMP2 chimera
ComponentsAB204 Activin A/BMP2 chimera
KeywordsCYTOKINE / cysteine knot / ActRII / BMPRIa / Secreted
Function / homology
Function and homology information


cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / ameloblast differentiation / positive regulation of extracellular matrix constituent secretion / negative regulation of cardiac muscle cell differentiation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / aortic valve development / telencephalon regionalization / positive regulation of phosphatase activity / positive regulation of odontogenesis / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / pericardium development / lung vasculature development / BMP receptor complex / co-receptor binding / telencephalon development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / positive regulation of odontoblast differentiation / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / phosphatase activator activity / Transcriptional regulation by RUNX2 / positive regulation of astrocyte differentiation / Signaling by BMP / cellular response to BMP stimulus / cardiac muscle cell differentiation / cardiac muscle tissue morphogenesis / positive regulation of ossification / astrocyte differentiation / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / endocardial cushion morphogenesis / branching involved in ureteric bud morphogenesis / negative regulation of fat cell differentiation / bone mineralization / positive regulation of osteoblast proliferation / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / inner ear development / cellular response to organic cyclic compound / negative regulation of cell cycle / positive regulation of Wnt signaling pathway / positive regulation of fat cell differentiation / epithelial to mesenchymal transition / cell fate commitment / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / protein serine/threonine kinase activator activity / osteoclast differentiation / negative regulation of MAP kinase activity / skeletal system development / cytokine activity / negative regulation of smooth muscle cell proliferation / animal organ morphogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / response to bacterium / growth factor activity / protein destabilization / bone development / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / osteoblast differentiation / Regulation of RUNX2 expression and activity / positive regulation of protein binding / cell-cell signaling / heart development / in utero embryonic development / transcription by RNA polymerase II / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / positive regulation of cell migration / inflammatory response / positive regulation of apoptotic process / positive regulation of protein phosphorylation
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.139 Å
AuthorsEsquivies, L.
CitationJournal: J.Bone Miner.Res. / Year: 2014
Title: An Activin A/BMP2 Chimera, AB204, Displays Bone-Healing Properties Superior to Those of BMP2.
Authors: Yoon, B.H. / Esquivies, L. / Ahn, C. / Gray, P.C. / Ye, S.K. / Kwiatkowski, W. / Choe, S.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AB204 Activin A/BMP2 chimera


Theoretical massNumber of molelcules
Total (without water)13,0901
Polymers13,0901
Non-polymers00
Water36020
1
A: AB204 Activin A/BMP2 chimera

A: AB204 Activin A/BMP2 chimera


Theoretical massNumber of molelcules
Total (without water)26,1802
Polymers26,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area2520 Å2
ΔGint-26 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.615, 32.615, 147.358
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is generated by Y-1,X,-Z

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Components

#1: Protein AB204 Activin A/BMP2 chimera


Mass: 13090.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12643*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CHIMERA SEQUENCE MATCHES TO HUMAN BMP2 P12643 AND HUMAN ACTIVIN/INHIBIN A CHAIN. MATCHING TO ...THE CHIMERA SEQUENCE MATCHES TO HUMAN BMP2 P12643 AND HUMAN ACTIVIN/INHIBIN A CHAIN. MATCHING TO THE ABOVE TWO ARE NOT DISTINCTLY SEPARATED AT ANY CERTAIN RESIDUE THUS NO DBREF IS GIVEN.

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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: 1.73 Å3/Da / Density % sol: 28.84 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M LiSO4, 0.1 M Tris, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.139→147.358 Å / Num. all: 5395 / Num. obs: 5395 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 23.2
Reflection shellResolution: 2.139→2.194 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.248 / % possible all: 76.7

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.139→28.245 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.918 / SU ML: 0.24 / σ(F): 1.39 / Phase error: 27.68 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2643 244 4.57 %
Rwork0.219 --
obs0.2213 5342 96.25 %
all-5106 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.821 Å2
Baniso -1Baniso -2Baniso -3
1-11.97 Å20 Å20 Å2
2--11.97 Å20 Å2
3----23.94 Å2
Refinement stepCycle: LAST / Resolution: 2.139→28.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 0 20 842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003847
X-RAY DIFFRACTIONf_angle_d0.7671147
X-RAY DIFFRACTIONf_dihedral_angle_d14.453310
X-RAY DIFFRACTIONf_chiral_restr0.048125
X-RAY DIFFRACTIONf_plane_restr0.005149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1388-2.69440.31131140.23612384X-RAY DIFFRACTION92
2.6944-28.24790.25371300.21452714X-RAY DIFFRACTION100
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)
14.45450.8492-1.43544.2672-2.19686.44940.37430.0762-0.4557-0.15510.16980.21820.94410.1439-0.34310.35440.0219-0.02040.2233-0.00140.2522-20.98137.6733-15.3923
21.60092.0145-0.3843.75770.8698.55690.4508-0.0164-0.5740.3239-0.148-0.85080.63370.3282-0.20440.4808-0.0074-0.14950.30240.07490.3764-24.61686.8310.4814
32.97711.7621-2.55154.4341-2.99348.71250.0593-0.08350.3764-0.0478-0.0733-0.0463-0.59350.14520.04270.33550.004-0.01630.2121-0.00930.289-19.763318.3736-14.9522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 114 )

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