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- PDB-5ty4: MicroED structure of a complex between monomeric TGF-b and its re... -

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Basic information

Entry
Database: PDB / ID: 5ty4
TitleMicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution
Components
  • TGF-beta receptor type-2
  • mmTGF-b2-7m
KeywordsTRANSFERASE
Function / homology
Function and homology information


regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / substantia propria of cornea development / ascending aorta morphogenesis / cardioblast differentiation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / substantia propria of cornea development / ascending aorta morphogenesis / cardioblast differentiation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis / bronchus morphogenesis / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / cardiac right ventricle morphogenesis / miRNA transport / regulation of transforming growth factor beta2 production / transforming growth factor beta ligand-receptor complex / atrial septum morphogenesis / pharyngeal arch artery morphogenesis / positive regulation of heart contraction / type III transforming growth factor beta receptor binding / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / Langerhans cell differentiation / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / glial cell migration / cardiac left ventricle morphogenesis / secondary palate development / somatic stem cell division / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of integrin biosynthetic process / atrial septum primum morphogenesis / endocardial cushion fusion / positive regulation of T cell tolerance induction / membranous septum morphogenesis / heart valve morphogenesis / TGFBR3 regulates TGF-beta signaling / lung lobe morphogenesis / positive regulation of NK T cell differentiation / cardiac epithelial to mesenchymal transition / eye development / signaling / positive regulation of stress-activated MAPK cascade / activin receptor complex / embryonic digestive tract development / transforming growth factor beta receptor binding / cranial skeletal system development / neural retina development / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / activation of protein kinase activity / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / transforming growth factor beta receptor activity, type III / activin binding / regulation of stem cell proliferation / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / activin receptor signaling pathway / glycosaminoglycan binding / cell-cell junction organization / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of Ras protein signal transduction / regulation of stem cell differentiation / response to cholesterol / embryonic cranial skeleton morphogenesis / transforming growth factor beta binding / collagen fibril organization / kinase activator activity / aortic valve morphogenesis / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / embryo development ending in birth or egg hatching / atrioventricular valve morphogenesis / lens development in camera-type eye / odontogenesis / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / artery morphogenesis / endocardial cushion morphogenesis / cardiac muscle cell proliferation / Molecules associated with elastic fibres / dopamine biosynthetic process
Similarity search - Function
Transforming growth factor beta-2 proprotein / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / 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-2 proprotein / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / 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. / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
TGF-beta receptor type-2 / Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.9 Å
AuthorsWeiss, S.C. / de la Cruz, M.J. / Hattne, J. / Shi, D. / Reyes, F.E. / Callero, G. / Gonen, T.
CitationJournal: 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 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Category: diffrn_detector / pdbx_related_exp_data_set
Item: _diffrn_detector.type / _pdbx_related_exp_data_set.data_reference
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Oct 4, 2023Group: 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
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Assembly

Deposited unit
A: TGF-beta receptor type-2
B: mmTGF-b2-7m


Theoretical massNumber of molelcules
Total (without water)22,8652
Polymers22,8652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-2 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.530, 71.330, 79.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TGF-beta receptor type-2 / TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta receptor type II / TbetaR-II


Mass: 11788.519 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Production host: Escherichia coli (E. coli)
References: UniProt: P37173, receptor protein serine/threonine kinase
#2: Protein mmTGF-b2-7m


Mass: 11076.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61812*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Complex between monomeric TGF-b and its receptor, TbRII
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.019072 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer componentConc.: 100 mM / Name: HEPES
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 ul 20 mg/mL protein + 0.25 ul mother liquor + 0.2 ul seed stock in 100 mM HEPES/NaOH pH 7.5, 45% MPD

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 0.004 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 353 / Num. of grids imaged: 2 / Num. of real images: 353
Image scansSampling size: 0.0311999992 µm / Width: 2048 / Height: 2048
EM diffractionCamera length: 2000 mm
EM diffraction shellResolution: 2.9→3.65 Å / Fourier space coverage: 69.1 % / Multiplicity: 3.9 / Num. of structure factors: 1884 / Phase residual: 46.4 °
EM diffraction statsFourier space coverage: 71.9 % / High resolution: 2.9 Å / Num. of intensities measured: 14911 / Num. of structure factors: 3884 / Phase error: 30.99 ° / Phase residual: 43.53 ° / Phase error rejection criteria: 0 / Rmerge: 0.293 / Rsym: 0.293
DiffractionMean temperature: 293 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: OTHER / Wavelength: 0.0250793397 Å
DetectorType: TVIPS TEMCAM-F416 / Detector: CMOS / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0250793397 Å / Relative weight: 1
ReflectionResolution: 2.9→26.64 Å / Num. obs: 3884 / % possible obs: 71.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 64 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.293 / Rsym value: 0.293 / Net I/σ(I): 3.3
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 2.024 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.255 / % possible all: 71.3

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
MOSFLM7.1.0data reduction
Aimless0.5.27data scaling
PHASER2.6.0phasing
EM software
IDNameVersionCategoryDetails
1EM-Menu4.0.9.75image acquisition
5iMosflm/MOSFLM7.2.1diffraction indexing
6Phaser2.6.0model fitting
7MOLREP11.4.05otherphasing
8PHENIX1.1model refinement
9Phaser2.6.0molecular replacement
11POINTLESS1.10.26symmetry determination
12AIMLESS0.5.27crystallography merging
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 41.5298 Å / B: 71.3297 Å / C: 79.5082 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KTZ

1ktz


Resolution: 2.9→26.64 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / Phase error: 30.99
RfactorNum. reflection% reflection
Rfree0.328 290 7.54 %
Rwork0.2919 --
obs0.2948 3848 68.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 0 0 1327
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0121366
ELECTRON CRYSTALLOGRAPHYf_angle_d1.5731847
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d19.181864
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.067200
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.009231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.65230.36871360.36111748ELECTRON CRYSTALLOGRAPHY69
3.6523-26.640.31331540.26391810ELECTRON CRYSTALLOGRAPHY69

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