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Yorodumi- 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 | ||||||
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Title | MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
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 / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / uterine wall breakdown / transforming growth factor beta receptor activity, type II ...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 / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / uterine wall breakdown / transforming growth factor beta receptor activity, type II / cardioblast differentiation / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / positive regulation of timing of catagen / growth plate cartilage chondrocyte growth / positive regulation of cardioblast differentiation / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / positive regulation of heart contraction / activin receptor activity / miRNA transport / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / regulation of transforming growth factor beta2 production / Langerhans cell differentiation / aorta morphogenesis / atrial septum morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / signaling / transforming growth factor beta receptor activity / secondary palate development / cardiac left ventricle morphogenesis / glial cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / somatic stem cell division / endocardial cushion fusion / positive regulation of T cell tolerance induction / heart valve morphogenesis / membranous septum morphogenesis / atrial septum primum morphogenesis / lung lobe morphogenesis / positive regulation of integrin biosynthetic process / positive regulation of NK T cell differentiation / cardiac epithelial to mesenchymal transition / eye development / cranial skeletal system development / positive regulation of stress-activated MAPK cascade / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / neural retina development / receptor protein serine/threonine kinase / pulmonary valve morphogenesis / transmembrane receptor protein serine/threonine kinase activity / activin binding / myeloid dendritic cell differentiation / type I transforming growth factor beta receptor binding / outflow tract septum morphogenesis / positive regulation of CD4-positive, alpha-beta T cell proliferation / SMAD protein signal transduction / regulation of stem cell differentiation / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / kinase activator activity / glycosaminoglycan binding / negative regulation of Ras protein signal transduction / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / collagen fibril organization / aortic valve morphogenesis / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / embryo development ending in birth or egg hatching / odontogenesis / lens development in camera-type eye / Molecules associated with elastic fibres / hair follicle development / atrioventricular valve morphogenesis / embryonic hemopoiesis / dopamine biosynthetic process / cardiac muscle cell proliferation / positive regulation of mesenchymal cell proliferation / artery morphogenesis / trachea formation / endocardial cushion morphogenesis / hair follicle morphogenesis / branching involved in blood vessel morphogenesis / smoothened signaling pathway / ventricular septum morphogenesis / generation of neurons / positive regulation of Notch signaling pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Weiss, S.C. / de la Cruz, M.J. / Hattne, J. / Shi, D. / Reyes, F.E. / Callero, G. / Gonen, T. | ||||||
Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ty4.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ty4.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ty4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ty4_validation.pdf.gz | 626.9 KB | Display | wwPDB validaton report |
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Full document | 5ty4_full_validation.pdf.gz | 626.5 KB | Display | |
Data in XML | 5ty4_validation.xml.gz | 8 KB | Display | |
Data in CIF | 5ty4_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/5ty4 ftp://data.pdbj.org/pub/pdb/validation_reports/ty/5ty4 | HTTPS FTP |
-Related structure data
Related structure data | 8472MC 8216C 8217C 8218C 8219C 8220C 8221C 8222C 5k7nC 5k7oC 5k7pC 5k7qC 5k7rC 5k7sC 5k7tC 1ktzS |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/368 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1 |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Complex between monomeric TGF-b and its receptor, TbRII Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.019072 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Buffer component | Conc.: 100 mM / Name: HEPES |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.24 % |
Crystal grow | Temperature: 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 |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average 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 scans | Sampling size: 0.0311999992 µm / Width: 2048 / Height: 2048 |
EM diffraction | Camera length: 2000 mm |
EM diffraction shell | Resolution: 2.9→3.65 Å / Fourier space coverage: 69.1 % / Multiplicity: 3.9 / Num. of structure factors: 1884 / Phase residual: 46.4 ° |
EM diffraction stats | Fourier 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 |
Diffraction | Mean temperature: 293 K |
Diffraction source | Source: ELECTRON MICROSCOPE / Type: OTHER / Wavelength: 0.0250793397 Å |
Detector | Type: TVIPS TEMCAM-F416 / Detector: CMOS / Date: May 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron |
Radiation wavelength | Wavelength: 0.0250793397 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
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EM software |
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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 correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KTZ Resolution: 2.9→26.64 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / Phase error: 30.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→26.64 Å
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Refine LS restraints |
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LS refinement shell |
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