[English] 日本語
Yorodumi
- PDB-5ty4: MicroED structure of a complex between monomeric TGF-b and its re... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of activation-induced cell death of T cells / cardioblast differentiation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown ...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 / positive regulation of activation-induced cell death of T cells / cardioblast differentiation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / positive regulation of timing of catagen / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / positive regulation of cardioblast differentiation / 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 / type III transforming growth factor beta receptor binding / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of heart contraction / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / activation-induced cell death of T cells / glial cell migration / cardiac left ventricle morphogenesis / positive regulation of extracellular matrix disassembly / secondary palate development / negative regulation of macrophage cytokine production / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / somatic stem cell division / positive regulation of integrin biosynthetic process / atrial septum primum morphogenesis / endocardial cushion fusion / membranous septum morphogenesis / positive regulation of T cell tolerance induction / heart valve morphogenesis / positive regulation of NK T cell differentiation / negative regulation of cartilage development / cardiac epithelial to mesenchymal transition / signaling / TGFBR3 regulates TGF-beta signaling / positive regulation of stress-activated MAPK cascade / neuron fate commitment / pericyte cell differentiation / activin receptor complex / activin receptor activity, type I / lung lobe morphogenesis / transforming growth factor beta receptor binding / eye development / neural retina development / embryonic digestive tract development / type II transforming growth factor beta receptor binding / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / regulation of stem cell proliferation / pulmonary valve morphogenesis / activin binding / cranial skeletal system development / TGFBR1 LBD Mutants in Cancer / SMAD protein signal transduction / type I transforming growth factor beta receptor binding / myeloid dendritic cell differentiation / embryonic cranial skeleton morphogenesis / glycosaminoglycan binding / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / negative regulation of Ras protein signal transduction / positive regulation of CD4-positive, alpha-beta T cell proliferation / embryo development ending in birth or egg hatching / regulation of stem cell differentiation / response to cholesterol / outflow tract septum morphogenesis / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell-cell junction organization / transforming growth factor beta binding / collagen fibril organization / kinase activator activity / embryonic limb morphogenesis / aortic valve morphogenesis / lens development in camera-type eye / positive regulation of cell adhesion mediated by integrin / atrioventricular valve morphogenesis / face morphogenesis / odontogenesis / positive regulation of mesenchymal cell proliferation / embryonic hemopoiesis / artery morphogenesis / endocardial cushion morphogenesis
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8472
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8472
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more