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- PDB-5tx6: Structure of TGF-beta2 derivative with deletion of residues 52-71... -

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Basic information

Entry
Database: PDB / ID: 5tx6
TitleStructure of TGF-beta2 derivative with deletion of residues 52-71 and 10 single amino acid mutations (mmTGF-beta2-7M)
ComponentsTransforming growth factor beta-2
KeywordsCYTOKINE / Growth Factor
Function / homology
Function and homology information


positive regulation of activation-induced cell death of T cells / positive regulation of GTP binding / TGFBR3 regulates TGF-beta signaling / Molecules associated with elastic fibres / regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / embryonic neurocranium morphogenesis ...positive regulation of activation-induced cell death of T cells / positive regulation of GTP binding / TGFBR3 regulates TGF-beta signaling / Molecules associated with elastic fibres / regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / embryonic neurocranium morphogenesis / cardioblast differentiation / positive regulation of timing of catagen / TGF-beta receptor signaling activates SMADs / negative regulation of keratinocyte differentiation / positive regulation of cardioblast differentiation / negative regulation of cartilage development / somatic stem cell division / regulation of extracellular matrix organization / atrial septum morphogenesis / heart valve morphogenesis / cardiac right ventricle morphogenesis / pericyte cell differentiation / transforming growth factor beta complex / regulation of transforming growth factor beta2 production / uterus development / positive regulation of heart contraction / pharyngeal arch artery morphogenesis / negative regulation of macrophage cytokine production / type III transforming growth factor beta receptor binding / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / glial cell migration / positive regulation of stress-activated MAPK cascade / cardiac left ventricle morphogenesis / salivary gland morphogenesis / atrial septum primum morphogenesis / membranous septum morphogenesis / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of integrin biosynthetic process / secondary palate development / endocardial cushion fusion / hair follicle development / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of extracellular matrix disassembly / cardiac epithelial to mesenchymal transition / cranial skeletal system development / embryonic limb morphogenesis / neuron fate commitment / signaling / Platelet degranulation / embryonic digestive tract development / cell-cell junction organization / type II transforming growth factor beta receptor binding / eye development / pulmonary valve morphogenesis / transforming growth factor beta receptor binding / negative regulation of Ras protein signal transduction / neural retina development / atrioventricular valve morphogenesis / ventricular trabecula myocardium morphogenesis / outflow tract septum morphogenesis / collagen fibril organization / blood vessel development / endocardial cushion morphogenesis / hair follicle morphogenesis / face morphogenesis / positive regulation of cell adhesion mediated by integrin / positive regulation of cell division / cartilage condensation / negative regulation of release of sequestered calcium ion into cytosol / ventricular septum morphogenesis / blood vessel remodeling / neural tube closure / dopamine biosynthetic process / inner ear development / positive regulation of Notch signaling pathway / neuron development / hemopoiesis / basement membrane / outflow tract morphogenesis / positive regulation of epithelial cell migration / response to progesterone / positive regulation of SMAD protein signal transduction / cardiac muscle cell proliferation / heart morphogenesis / epithelial to mesenchymal transition / skeletal system development / transforming growth factor beta receptor signaling pathway / extrinsic apoptotic signaling pathway / positive regulation of epithelial to mesenchymal transition / extracellular matrix organization / cell morphogenesis / neutrophil chemotaxis / kidney development / negative regulation of angiogenesis / positive regulation of cell cycle / epithelial cell differentiation / male gonad development / secretory granule / axon guidance / cytokine activity
Similarity search - Function
Transforming growth factor beta-2 proprotein / Transforming growth factor-beta / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...Transforming growth factor beta-2 proprotein / Transforming growth factor-beta / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.746 Å
AuthorsPetrunak, E.M. / Hinck, A.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58670 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA172886 United States
Robert A. Welch FoundationAQ1842 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: An engineered transforming growth factor beta (TGF-beta ) monomer that functions as a dominant negative to block TGF-beta signaling.
Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / ...Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / Barnes, C.O. / Sulea, T. / Calero, G. / Hart, P.J. / Hart, M.J. / Demeler, B. / Hinck, A.P.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _refine.pdbx_starting_model / _struct_conn.pdbx_dist_value / _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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Transforming growth factor beta-2
A: Transforming growth factor beta-2
C: Transforming growth factor beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9374
Polymers31,8973
Non-polymers401
Water1,13563
1
A: Transforming growth factor beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6722
Polymers10,6321
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)10,6321
Polymers10,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)10,6321
Polymers10,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.744, 81.744, 80.926
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transforming growth factor beta-2 / TGF-beta-2


Mass: 10632.378 Da / Num. of mol.: 3 / Fragment: UNP residues 303-414
Mutation: K25R, R26K, L51R, A74K, C77S, L89V, I92V, K94R, T95K, I98V
Source method: isolated from a genetically manipulated source
Details: Residues 52-71 were deleted. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tgfb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P27090
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100 mM sodium acetate trihydrate pH 4.7, 25% 2-propanol, 400 mM calcium chloride dihydrate, 0.5% n-octyl-beta-D-glucoside
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.746→36.483 Å / Num. obs: 10929 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rpim(I) all: 0.055 / Rsym value: 0.132 / Net I/σ(I): 16.4
Reflection shellResolution: 2.746→2.89 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4 / Rpim(I) all: 0.232 / Rsym value: 0.463 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.746→36.483 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 421 4.96 %
Rwork0.2127 --
obs0.2157 8493 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.746→36.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 1 63 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032148
X-RAY DIFFRACTIONf_angle_d0.7632889
X-RAY DIFFRACTIONf_dihedral_angle_d14.539798
X-RAY DIFFRACTIONf_chiral_restr0.029304
X-RAY DIFFRACTIONf_plane_restr0.004369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7461-3.14330.29451290.25732654X-RAY DIFFRACTION100
3.1433-3.95950.26861440.20052654X-RAY DIFFRACTION100
3.9595-36.48630.26371480.20232764X-RAY DIFFRACTION100

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