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- PDB-6i9j: Human transforming growth factor beta2 in a tetragonal crystal form -

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Basic information

Entry
Database: PDB / ID: 6i9j
TitleHuman transforming growth factor beta2 in a tetragonal crystal form
ComponentsTransforming growth factor beta-2 proprotein
KeywordsCYTOKINE / growth factor / cysteine-knot cytokines / small proteins / TGF-beta2 / cell growth
Function / homology
Function and homology information


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 / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis ...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 / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / positive regulation of heart contraction / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / signaling / secondary palate development / positive regulation of stress-activated MAPK cascade / glial cell migration / somatic stem cell division / heart valve morphogenesis / atrial septum primum morphogenesis / endocardial cushion fusion / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / cardiac epithelial to mesenchymal transition / neural retina development / eye development / cranial skeletal system development / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / outflow tract septum morphogenesis / negative regulation of Ras protein signal transduction / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / collagen fibril organization / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / dopamine biosynthetic process / embryo development ending in birth or egg hatching / odontogenesis / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / generation of neurons / hair follicle morphogenesis / ventricular septum morphogenesis / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / activation of protein kinase activity / TGF-beta receptor signaling activates SMADs / inner ear development / uterus development / positive regulation of SMAD protein signal transduction / hemopoiesis / positive regulation of cell division / hair follicle development / ECM proteoglycans / neuron development / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of cell cycle / salivary gland morphogenesis / heart morphogenesis / extrinsic apoptotic signaling pathway / epithelial cell differentiation / negative regulation of angiogenesis / neutrophil chemotaxis / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / response to progesterone / kidney development / skeletal system development / cytokine activity / neural tube closure / positive regulation of protein secretion / growth factor activity / wound healing / cell morphogenesis / negative regulation of cell growth / response to wounding / positive regulation of miRNA transcription / male gonad development / positive regulation of neuron apoptotic process / positive regulation of immune response / negative regulation of epithelial cell proliferation / cell migration / Platelet degranulation / regulation of cell population proliferation / heart development / amyloid-beta binding / positive regulation of cell growth / collagen-containing extracellular matrix / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
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 / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...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 / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine
Similarity search - Domain/homology
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGomis-Ruth, F.X. / Marino-Puertas, L. / del Amo-Maestro, L. / Goulas, T.
Citation
Journal: Sci Rep / Year: 2019
Title: Recombinant production, purification, crystallization, and structure analysis of human transforming growth factor beta 2 in a new conformation.
Authors: Del Amo-Maestro, L. / Marino-Puertas, L. / Goulas, T. / Gomis-Ruth, F.X.
#1: Journal: Nature / Year: 1992
Title: An unusual feature revealed by the crystal structure at 2.2 A resolution of human transforming growth factor-beta 2.
Authors: Schlunegger, M.P. / Grutter, M.G.
#2: Journal: Science / Year: 1992
Title: Crystal structure of transforming growth factor-beta 2: an unusual fold for the superfamily.
Authors: Daopin, S. / Piez, K.A. / Ogawa, Y. / Davies, D.R.
#3: Journal: Protein Sci. / Year: 2014
Title: Structures of a pan-specific antagonist antibody complexed to different isoforms of TGFbeta reveal structural plasticity of antibody-antigen interactions.
Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / ...Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / Bird, J. / Qiu, H. / Pan, C.Q. / Edmunds, T. / Wei, R.R.
#4: Journal: 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.
#5: Journal: Nat Methods / Year: 2017
Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen /
Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.
History
DepositionNov 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Transforming growth factor beta-2 proprotein


Theoretical massNumber of molelcules
Total (without water)12,7331
Polymers12,7331
Non-polymers00
Water41423
1
A: Transforming growth factor beta-2 proprotein

A: Transforming growth factor beta-2 proprotein


Theoretical massNumber of molelcules
Total (without water)25,4652
Polymers25,4652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2400 Å2
ΔGint-27 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.570, 55.570, 70.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transforming growth factor beta-2 proprotein / Cetermin / Glioblastoma-derived T-cell suppressor factor / G-TSF


Mass: 12732.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Cell line (production host): Expi293F TM cells / Production host: Homo sapiens (human) / References: UniProt: P61812
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.14 Å3/Da / Density % sol: 42.51 % / Description: tetragonal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 20% isopropanol, 0.2M calcium chloride, 0.1M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→70.6 Å / Num. obs: 7919 / % possible obs: 100 % / Redundancy: 24.3 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.072 / Net I/σ(I): 23.4
Reflection shellResolution: 2→2.12 Å / Redundancy: 24.8 % / Rmerge(I) obs: 2.495 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.87 / Rrim(I) all: 2.546 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TGI

2tgi


Resolution: 2→43.66 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.253 407 5.14 %RANDOM
Rwork0.217 ---
obs0.218 7918 100 %-
Displacement parametersBiso mean: 66.21 Å2
Baniso -1Baniso -2Baniso -3
1--8.9235 Å20 Å20 Å2
2---8.9235 Å20 Å2
3---17.8471 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 23 913
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01919HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.181254HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d305SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes152HARMONIC5
X-RAY DIFFRACTIONt_it919HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion19.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion119SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1047SEMIHARMONIC4
LS refinement shellResolution: 2→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2753 -2.78 %
Rwork0.2524 385 -
all0.2528 396 -
obs--99.49 %
Refinement TLS params.Method: refined / Origin x: 3.5866 Å / Origin y: 12.9136 Å / Origin z: 8.6135 Å
111213212223313233
T0.1411 Å20.053 Å20.0021 Å2-0.0624 Å2-0.0082 Å2--0.0648 Å2
L1.9077 °2-1.1678 °2-1.7821 °2-0.3884 °20.9384 °2--2.258 °2
S-0.2523 Å °0.0055 Å °-0.1239 Å °0.0937 Å °0.1246 Å °0.0758 Å °0.3283 Å °0.1288 Å °0.1277 Å °
Refinement TLS groupSelection details: {A|303 - 414}

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