[English] 日本語
Yorodumi
- PDB-4ajv: Structure of mouse ZP-C domain of TGF-Beta-Receptor-3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ajv
TitleStructure of mouse ZP-C domain of TGF-Beta-Receptor-3
ComponentsTRANSFORMING GROWTH FACTOR BETA RECEPTOR TYPE 3
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


epicardial cell to mesenchymal cell transition / negative regulation of apoptotic process involved in morphogenesis / : / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / transforming growth factor beta receptor complex assembly / : / inhibin-betaglycan-ActRII complex / muscular septum morphogenesis ...epicardial cell to mesenchymal cell transition / negative regulation of apoptotic process involved in morphogenesis / : / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / transforming growth factor beta receptor complex assembly / : / inhibin-betaglycan-ActRII complex / muscular septum morphogenesis / definitive erythrocyte differentiation / response to follicle-stimulating hormone / coronary vasculature morphogenesis / visceral serous pericardium development / response to prostaglandin E / vasculogenesis involved in coronary vascular morphogenesis / transforming growth factor beta receptor activity / secondary palate development / ventricular compact myocardium morphogenesis / negative regulation of epithelial cell migration / collagen metabolic process / regulation of transforming growth factor beta receptor signaling pathway / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / regulation of protein binding / heart trabecula morphogenesis / activin binding / coronary vasculature development / heart trabecula formation / positive regulation of BMP signaling pathway / glycosaminoglycan binding / transforming growth factor beta binding / negative regulation of epithelial to mesenchymal transition / definitive hemopoiesis / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / ventricular septum morphogenesis / roof of mouth development / fibroblast growth factor binding / blood vessel development / positive regulation of transforming growth factor beta receptor signaling pathway / outflow tract morphogenesis / plasma membrane => GO:0005886 / SMAD binding / blastocyst development / epithelial to mesenchymal transition / blood vessel remodeling / vasculogenesis / BMP signaling pathway / coreceptor activity / positive regulation of cardiac muscle cell proliferation / blood vessel diameter maintenance / transforming growth factor beta receptor signaling pathway / extracellular matrix / liver development / PDZ domain binding / negative regulation of transforming growth factor beta receptor signaling pathway / osteoblast differentiation / negative regulation of epithelial cell proliferation / cell migration / positive regulation of NF-kappaB transcription factor activity / heparin binding / protein-containing complex assembly / angiogenesis / in utero embryonic development / membrane => GO:0016020 / receptor complex / intracellular signal transduction / immune response / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / cell surface / endoplasmic reticulum / extracellular space / cytoplasm
Similarity search - Function
Zona pellucida, ZP-C domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta receptor type 3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDiestel, U. / Resch, M. / Meinhardt, K. / Weiler, S. / Hellmann, T.V. / Nickel, J. / Eichler, J. / Muller, Y.A.
CitationJournal: Plos One / Year: 2013
Title: Identification of a Novel Tgf-Beta-Binding Site in the Zona Pellucida C-Terminal (Zp-C) Domain of Tgf-Beta-Receptor-3 (Tgfr-3).
Authors: Diestel, U. / Resch, M. / Meinhardt, K. / Weiler, S. / Hellmann, T.V. / Mueller, T.D. / Nickel, J. / Eichler, J. / Muller, Y.A.
History
DepositionFeb 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSFORMING GROWTH FACTOR BETA RECEPTOR TYPE 3


Theoretical massNumber of molelcules
Total (without water)19,0171
Polymers19,0171
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.660, 56.820, 60.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TRANSFORMING GROWTH FACTOR BETA RECEPTOR TYPE 3 / TGF-BETA RECEPTOR TYPE 3 / TGFR-3 / BETAGLYCAN / TRANSFORMING GROWTH FACTOR BETA RECEPTOR III / TGF- ...TGF-BETA RECEPTOR TYPE 3 / TGFR-3 / BETAGLYCAN / TRANSFORMING GROWTH FACTOR BETA RECEPTOR III / TGF-BETA RECEPTOR TYPE III


Mass: 19016.840 Da / Num. of mol.: 1 / Fragment: ZP-C DOMAIN, RESIDUES 591-757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK 293 EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: O88393
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.05 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M HEPES PH 6 TO 7, 0.2 M AMMONIUM ACETATE, 20 TO 30 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.7→38.32 Å / Num. obs: 4960 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QW9

3qw9


Resolution: 2.7→38.318 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 30.6 / Stereochemistry target values: ML / Details: RESIDUES 730-744 COULD NOT BE MODELED
RfactorNum. reflection% reflection
Rfree0.2958 271 5.5 %
Rwork0.22 --
obs0.2242 4959 99.28 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.046 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1--10.6555 Å20 Å20 Å2
2--21.8371 Å20 Å2
3----11.1816 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 0 9 1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171241
X-RAY DIFFRACTIONf_angle_d1.7531681
X-RAY DIFFRACTIONf_dihedral_angle_d17.933450
X-RAY DIFFRACTIONf_chiral_restr0.09193
X-RAY DIFFRACTIONf_plane_restr0.009215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-3.40170.36861420.24612288X-RAY DIFFRACTION100
3.4017-38.32210.26491290.20942400X-RAY DIFFRACTION99

+
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://pdbjlvh1.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