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Yorodumi- EMDB-8472: MicroED structure of a complex between monomeric TGF-b and its re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8472 | |||||||||
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Title | MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution | |||||||||
Map data | Complex between monomeric TGF-b and its receptor, TbRII | |||||||||
Sample |
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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 / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / ascending aorta morphogenesis / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / uterine wall breakdown ...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 / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / ascending aorta morphogenesis / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / uterine wall breakdown / bronchus morphogenesis / cardioblast differentiation / 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 / activin receptor activity / miRNA transport / Langerhans cell differentiation / 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 / atrial septum morphogenesis / aorta morphogenesis / positive regulation of heart contraction / 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 / positive regulation of stress-activated MAPK cascade / glial cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / somatic stem cell division / heart valve morphogenesis / endocardial cushion fusion / positive regulation of T cell tolerance induction / atrial septum primum morphogenesis / membranous septum 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 / neural retina development / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / regulation of stem cell proliferation / receptor protein serine/threonine kinase / myeloid dendritic cell differentiation / pulmonary valve morphogenesis / transmembrane receptor protein serine/threonine kinase activity / activin binding / type I transforming growth factor beta receptor binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / negative regulation of Ras protein signal transduction / ventricular trabecula myocardium morphogenesis / regulation of stem cell differentiation / cell-cell junction organization / SMAD protein signal transduction / glycosaminoglycan binding / kinase activator activity / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / aortic valve morphogenesis / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / dopamine biosynthetic process / embryo development ending in birth or egg hatching / odontogenesis / lens development in camera-type eye / Molecules associated with elastic fibres / embryonic hemopoiesis / atrioventricular valve morphogenesis / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / trachea formation / artery morphogenesis / endocardial cushion morphogenesis / generation of neurons / smoothened signaling pathway / branching involved in blood vessel morphogenesis / hair follicle morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / positive regulation of epithelial cell migration Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Weiss SC / de la Cruz MJ | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8472.map.gz | 604.4 KB | EMDB map data format | |
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Header (meta data) | emd-8472-v30.xml emd-8472.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_8472.png | 372.9 KB | ||
Filedesc metadata | emd-8472.cif.gz | 5.4 KB | ||
Filedesc structureFactors | emd_8472_sf.cif.gz | 955.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8472 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8472 | HTTPS FTP |
-Related structure data
Related structure data | 5ty4MC 8216C 8217C 8218C 8219C 8220C 8221C 8222C 5k7nC 5k7oC 5k7pC 5k7qC 5k7rC 5k7sC 5k7tC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8472.map.gz / Format: CCP4 / Size: 846.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Complex between monomeric TGF-b and its receptor, TbRII | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.94386 Å / Y: 0.93855 Å / Z: 0.94653 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex between monomeric TGF-b and its receptor, TbRII
Entire | Name: Complex between monomeric TGF-b and its receptor, TbRII |
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Components |
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-Supramolecule #1: Complex between monomeric TGF-b and its receptor, TbRII
Supramolecule | Name: Complex between monomeric TGF-b and its receptor, TbRII type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 19.072 KDa |
-Macromolecule #1: TGF-beta receptor type-2
Macromolecule | Name: TGF-beta receptor type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein serine/threonine kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.788519 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: FPQLCKFCDV RFSTCDNQKS CMSNCSITSI CEKPQEVCVA VWRKNDENIT LETVCHDPKL PYHDFILEDA ASPTCIMKEK KKPGETFFM CSCSSDECND NIIF UniProtKB: TGF-beta receptor type-2 |
-Macromolecule #2: mmTGF-b2-7m
Macromolecule | Name: mmTGF-b2-7m / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.076813 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: CCLRPLYIDF RKDLGWKWIH EPKGYNANFC AGACPYLWSS DTQHSRVLSL YNTINPEASA SPCCVSQDLE PLTIVYYVGR KPKVEQLSN MIVKSCKC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 / Component - Concentration: 100.0 mM / Component - Name: HEPES |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 2000 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 2 / Number real images: 353 / Number diffraction images: 353 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Crystallography statistics | Number intensities measured: 14911 / Number structure factors: 3884 / Fourier space coverage: 71.9 / R sym: 0.293 / R merge: 0.293 / Overall phase error: 30.99 / Overall phase residual: 43.53 / Phase error rejection criteria: 0 / High resolution: 2.9 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.9 Å / Shell - Low resolution: 3.65 Å / Shell - Number structure factors: 1884 / Shell - Phase residual: 46.4 / Shell - Fourier space coverage: 69.1 / Shell - Multiplicity: 3.9 |
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Molecular replacement | Software - Name: Phaser (ver. 2.6.0) |
Symmetry determination software list | Software - Name: POINTLESS (ver. 1.10.26) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
Merging software list | Software - Name: AIMLESS (ver. 0.5.27) |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER |
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Output model | PDB-5ty4: |