[English] 日本語
Yorodumi
- PDB-5tx6: Structure of TGF-beta2 derivative with deletion of residues 52-71... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tx6
TitleStructure of TGF-beta2 derivative with deletion of residues 52-71 and 10 single amino acid mutations (mmTGF-beta2-7M)
ComponentsTransforming growth factor beta-2
KeywordsCYTOKINE / Growth Factor
Function / homology
Function and homology information


positive regulation of GTP binding / TGFBR3 regulates TGF-beta signaling / Molecules associated with elastic fibres / 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 GTP binding / TGFBR3 regulates TGF-beta signaling / Molecules associated with elastic fibres / 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 / TGF-beta receptor signaling activates SMADs / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / pharyngeal arch artery morphogenesis / positive regulation of heart contraction / type III transforming growth factor beta receptor binding / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / activation-induced cell death of T cells / glial cell migration / negative regulation of keratinocyte differentiation / cardiac left ventricle morphogenesis / positive regulation of extracellular matrix disassembly / negative regulation of macrophage cytokine production / secondary palate development / somatic stem cell division / positive regulation of integrin biosynthetic process / atrial septum primum morphogenesis / endocardial cushion fusion / heart valve morphogenesis / membranous septum morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / negative regulation of cartilage development / cardiac epithelial to mesenchymal transition / signaling / positive regulation of stress-activated MAPK cascade / Platelet degranulation / neuron fate commitment / pericyte cell differentiation / embryonic digestive tract development / transforming growth factor beta receptor binding / eye development / neural retina development / regulation of extracellular matrix organization / pulmonary valve morphogenesis / type II transforming growth factor beta receptor binding / cranial skeletal system development / ventricular trabecula myocardium morphogenesis / negative regulation of Ras protein signal transduction / outflow tract septum morphogenesis / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell-cell junction organization / collagen fibril organization / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / atrioventricular valve morphogenesis / face morphogenesis / endocardial cushion morphogenesis / dopamine biosynthetic process / hair follicle morphogenesis / cartilage condensation / ventricular septum morphogenesis / blood vessel development / uterus development / inner ear development / outflow tract morphogenesis / hemopoiesis / positive regulation of cell division / blood vessel remodeling / positive regulation of SMAD protein signal transduction / positive regulation of epithelial cell migration / epithelial to mesenchymal transition / hair follicle development / cardiac muscle cell proliferation / neuron development / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / salivary gland morphogenesis / extrinsic apoptotic signaling pathway / positive regulation of cell cycle / extrinsic apoptotic signaling pathway in absence of ligand / neutrophil chemotaxis / epithelial cell differentiation / extracellular matrix organization / extracellular matrix / transforming growth factor beta receptor signaling pathway / response to progesterone / axon guidance / skeletal system development / positive regulation of protein secretion / regulation of actin cytoskeleton organization / neural tube closure / growth factor activity / kidney development / wound healing / negative regulation of cell growth / cell morphogenesis / positive regulation of immune response
Similarity search - Function
Transforming growth factor beta-2 proprotein / 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 ...Transforming growth factor beta-2 proprotein / 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. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.746 Å
AuthorsPetrunak, E.M. / Hinck, A.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58670 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA172886 United States
Robert A. Welch FoundationAQ1842 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: An engineered transforming growth factor beta (TGF-beta ) monomer that functions as a dominant negative to block TGF-beta signaling.
Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / ...Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / Barnes, C.O. / Sulea, T. / Calero, G. / Hart, P.J. / Hart, M.J. / Demeler, B. / Hinck, A.P.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_starting_model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Transforming growth factor beta-2
A: Transforming growth factor beta-2
C: Transforming growth factor beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9374
Polymers31,8973
Non-polymers401
Water1,13563
1
A: Transforming growth factor beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6722
Polymers10,6321
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)10,6321
Polymers10,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)10,6321
Polymers10,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.744, 81.744, 80.926
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Transforming growth factor beta-2 / TGF-beta-2


Mass: 10632.378 Da / Num. of mol.: 3 / Fragment: UNP residues 303-414
Mutation: K25R, R26K, L51R, A74K, C77S, L89V, I92V, K94R, T95K, I98V
Source method: isolated from a genetically manipulated source
Details: Residues 52-71 were deleted. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tgfb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P27090
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100 mM sodium acetate trihydrate pH 4.7, 25% 2-propanol, 400 mM calcium chloride dihydrate, 0.5% n-octyl-beta-D-glucoside
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.746→36.483 Å / Num. obs: 10929 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rpim(I) all: 0.055 / Rsym value: 0.132 / Net I/σ(I): 16.4
Reflection shellResolution: 2.746→2.89 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4 / Rpim(I) all: 0.232 / Rsym value: 0.463 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.746→36.483 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 421 4.96 %
Rwork0.2127 --
obs0.2157 8493 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.746→36.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 1 63 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032148
X-RAY DIFFRACTIONf_angle_d0.7632889
X-RAY DIFFRACTIONf_dihedral_angle_d14.539798
X-RAY DIFFRACTIONf_chiral_restr0.029304
X-RAY DIFFRACTIONf_plane_restr0.004369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7461-3.14330.29451290.25732654X-RAY DIFFRACTION100
3.1433-3.95950.26861440.20052654X-RAY DIFFRACTION100
3.9595-36.48630.26371480.20232764X-RAY DIFFRACTION100

+
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