[English] 日本語
Yorodumi
- PDB-1tgk: HUMAN TRANSFORMING GROWTH FACTOR BETA 3, CRYSTALLIZED FROM PEG 4000 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tgk
TitleHUMAN TRANSFORMING GROWTH FACTOR BETA 3, CRYSTALLIZED FROM PEG 4000
ComponentsTRANSFORMING GROWTH FACTOR BETA 3
KeywordsGROWTH FACTOR / MITOGEN / GLYCOPROTEIN
Function / homology
Function and homology information


frontal suture morphogenesis / uterine wall breakdown / detection of hypoxia / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding ...frontal suture morphogenesis / uterine wall breakdown / detection of hypoxia / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / mammary gland development / cell-cell junction organization / digestive tract development / transforming growth factor beta binding / face morphogenesis / odontogenesis / Molecules associated with elastic fibres / positive regulation of filopodium assembly / lung alveolus development / TGF-beta receptor signaling activates SMADs / inner ear development / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of SMAD protein signal transduction / positive regulation of cell division / ECM proteoglycans / positive regulation of collagen biosynthetic process / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / positive regulation of stress fiber assembly / T-tubule / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / response to progesterone / female pregnancy / cytokine activity / positive regulation of protein secretion / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / response to estrogen / Platelet degranulation / regulation of cell population proliferation / collagen-containing extracellular matrix / in utero embryonic development / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / response to hypoxia / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Transforming growth factor beta-3 / 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-3 / 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-3 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.3 Å
AuthorsMittl, P.R.E. / Priestle, J.P. / Gruetter, M.G.
Citation
Journal: Protein Sci. / Year: 1996
Title: The crystal structure of TGF-beta 3 and comparison to TGF-beta 2: implications for receptor binding.
Authors: Mittl, P.R. / Priestle, J.P. / Cox, D.A. / McMaster, G. / Cerletti, N. / Grutter, M.G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Crystal Structure of Human Transforming Growth Factor Beta 2 at 1.95 A Resolution
Authors: Schlunegger, M.P. / Grutter, M.G.
History
DepositionJul 10, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSFORMING GROWTH FACTOR BETA 3


Theoretical massNumber of molelcules
Total (without water)12,7351
Polymers12,7351
Non-polymers00
Water0
1
A: TRANSFORMING GROWTH FACTOR BETA 3

A: TRANSFORMING GROWTH FACTOR BETA 3


Theoretical massNumber of molelcules
Total (without water)25,4692
Polymers25,4692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+3/21
Buried area2420 Å2
ΔGint-27 kcal/mol
Surface area11530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.800, 77.800, 143.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein TRANSFORMING GROWTH FACTOR BETA 3 / / TGF-BETA3


Mass: 12734.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: STRAIN DEPOSITED AT DEUTSCHE SAMMLUNG VON MIKROORGANISMEN, MASCHENRODER WEG 1B, 3300 BRAUNSCHWEIG, GERMANY, ACCESSION NUMBER DSM 5658
Gene: HTGF-BETA3 / Plasmid: PPLMU / Gene (production host): HTGF-BETA3 / Production host: Escherichia coli (E. coli) / Strain (production host): LC137 / References: UniProt: P10600

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 74.94 %
Crystal growDetails: PEG 4000
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 8.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5-3 mg/mlprotein1drop
25 mMacetic acid1drop
315 %(w/v)PEG40001drop
4100 mMmagnesium chloride1drop
550 mMTris-HCl1droppH8.4
630 %(w/v)PEG40001reservoir
7200 mMmagnesium chloride1reservoir
8100 mMTris-HCl1reservoirpH8.4

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 23, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 4232 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.132
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 9999 Å
Reflection shell
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 3.36 Å / % possible obs: 100 %

-
Processing

Software
NameVersionClassification
MADNESdata collection
ROTAVATA-AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementResolution: 3.3→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.228 -
obs0.228 4052
Displacement parametersBiso mean: 40.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 0 890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.92
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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