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- EMDB-8472: MicroED structure of a complex between monomeric TGF-b and its re... -

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Basic information

Entry
Database: EMDB / ID: EMD-8472
TitleMicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution
Map dataComplex between monomeric TGF-b and its receptor, TbRII
Sample
  • Complex: Complex between monomeric TGF-b and its receptor, TbRII
    • Protein or peptide: TGF-beta receptor type-2
    • Protein or peptide: 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. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / 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
Similarity search - Domain/homology
TGF-beta receptor type-2 / Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodelectron crystallography / cryo EM / Resolution: 2.9 Å
AuthorsWeiss SC / de la Cruz MJ
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
Header (metadata) releaseJun 22, 2016-
Map releaseJun 22, 2016-
DepositionNov 18, 2016-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01299
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01299
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ty4
  • Surface level: 0.01299
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ty4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8472.png

Downloads & links

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Map

FileDownload / File: emd_8472.map.gz / Format: CCP4 / Size: 846.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex between monomeric TGF-b and its receptor, TbRII
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.95 Å/pix.
x 49 pix.
= 79.508 Å		0.94 Å/pix.
x 52 pix.
= 41.53 Å		0.94 Å/pix.
x 85 pix.
= 71.33 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.94386 Å / Y: 0.93855 Å / Z: 0.94653 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01299 / Movie #1: 0.01299
Minimum - Maximum-0.044779353 - 0.067389965
Average (Standard dev.)-0.0000074777117 (±0.008660839)
SymmetrySpace group: 19
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-34-26-36
Dimensions528549
Spacing447684
CellA: 41.5298 Å / B: 71.3297 Å / C: 79.5082 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.943863636363640.938552631578950.94652380952381
M x/y/z447684
origin x/y/z0.0000.0000.000
length x/y/z41.53071.33079.508
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S213
start NC/NR/NS-26-34-36
NC/NR/NS855249
D min/max/mean-0.0450.067-0.000

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Supplemental data

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Sample components

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Entire : Complex between monomeric TGF-b and its receptor, TbRII

EntireName: Complex between monomeric TGF-b and its receptor, TbRII
Components
  • Complex: Complex between monomeric TGF-b and its receptor, TbRII
    • Protein or peptide: TGF-beta receptor type-2
    • Protein or peptide: mmTGF-b2-7m

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Supramolecule #1: Complex between monomeric TGF-b and its receptor, TbRII

SupramoleculeName: Complex between monomeric TGF-b and its receptor, TbRII
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.072 KDa

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Macromolecule #1: TGF-beta receptor type-2

MacromoleculeName: TGF-beta receptor type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein serine/threonine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.788519 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FPQLCKFCDV RFSTCDNQKS CMSNCSITSI CEKPQEVCVA VWRKNDENIT LETVCHDPKL PYHDFILEDA ASPTCIMKEK KKPGETFFM CSCSSDECND NIIF

UniProtKB: TGF-beta receptor type-2

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Macromolecule #2: mmTGF-b2-7m

MacromoleculeName: mmTGF-b2-7m / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.076813 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CCLRPLYIDF RKDLGWKWIH EPKGYNANFC AGACPYLWSS DTQHSRVLSL YNTINPEASA SPCCVSQDLE PLTIVYYVGR KPKVEQLSN MIVKSCKC

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 7.5 / Component - Concentration: 100.0 mM / Component - Name: HEPES
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm 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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 2000 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: Phaser (ver. 2.6.0)
Symmetry determination software listSoftware - Name: POINTLESS (ver. 1.10.26)
Merging software listSoftware - Name: AIMLESS (ver. 0.5.27)
Crystallography statisticsNumber 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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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-5ty4:
MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution

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