[English] 日本語
Yorodumi
- PDB-6fwx: Chimeric titin Z1Z2-Z1Z2 tandem (Z1212) functionalized with a GRG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fwx
TitleChimeric titin Z1Z2-Z1Z2 tandem (Z1212) functionalized with a GRGDS exogenous peptide from fibronectin
ComponentsTitin,Titin,Titin
KeywordsSTRUCTURAL PROTEIN / titin / Z1Z2
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction / mitotic chromosome condensation / cardiac muscle hypertrophy / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / striated muscle contraction / protein kinase A signaling / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulins / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMayans, O. / Fleming, J. / Hill, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BBRSC and JRI OrthopaedicsBB/I01666X/1 United Kingdom
Citation
Journal: Adv. Mater. Weinheim / Year: 2019
Title: Self-Assembling Proteins as High-Performance Substrates for Embryonic Stem Cell Self-Renewal.
Authors: Hill, C.J. / Fleming, J.R. / Mousavinejad, M. / Nicholson, R. / Tzokov, S.B. / Bullough, P.A. / Bogomolovas, J. / Morgan, M.R. / Mayans, O. / Murray, P.
#1: Journal: Int J Mol Sci / Year: 2019
Title: The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications.
Authors: Nesterenko, Y. / Hill, C.J. / Fleming, J.R. / Murray, P. / Mayans, O.
History
DepositionMar 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author / reflns / Item: _reflns.percent_possible_obs
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Titin,Titin,Titin
B: Titin,Titin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9934
Polymers83,8692
Non-polymers1242
Water0
1
A: Titin,Titin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0593
Polymers41,9341
Non-polymers1242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin,Titin,Titin


Theoretical massNumber of molelcules
Total (without water)41,9341
Polymers41,9341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.400, 134.400, 134.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Titin,Titin,Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 41934.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% [v/v] isopropanol, 100 mM Na2HPO4 pH 4.2, 200 mM LiSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.974 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 3→41.8 Å / Num. obs: 17993 / % possible obs: 99 % / Redundancy: 4.1 % / Net I/σ(I): 9.26
Reflection shellResolution: 3→3.108 Å / Rmerge(I) obs: 1.803 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1813 / CC1/2: 0.162 / Rrim(I) all: 2.079

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A38

2a38


Resolution: 3→41.798 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 30.67
RfactorNum. reflection% reflection
Rfree0.2255 910 5.06 %
Rwork0.1995 --
obs0.2008 17985 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→41.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 8 0 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022976
X-RAY DIFFRACTIONf_angle_d0.4614050
X-RAY DIFFRACTIONf_dihedral_angle_d14.3131791
X-RAY DIFFRACTIONf_chiral_restr0.041479
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0003-3.18820.48021520.42552878X-RAY DIFFRACTION100
3.1882-3.43430.31671500.31652819X-RAY DIFFRACTION99
3.4343-3.77970.31081540.26612833X-RAY DIFFRACTION100
3.7797-4.32610.21821490.18582863X-RAY DIFFRACTION99
4.3261-5.44860.19411500.16112833X-RAY DIFFRACTION100
5.4486-41.80180.19361550.1812849X-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://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