[English] 日本語
Yorodumi
- PDB-4jnw: Bacterially expressed Titin Kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jnw
TitleBacterially expressed Titin Kinase
ComponentsTitin
KeywordsTRANSFERASE / muscle cytoskeleton
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy / mitotic chromosome condensation / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / actinin binding / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / response to calcium ion / Z disc / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBogomolovas, J. / Labeit, S. / Mayans, O.
Citation
Journal: Open Biol / Year: 2014
Title: Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line.
Authors: Bogomolovas, J. / Gasch, A. / Simkovic, F. / Rigden, D.J. / Labeit, S. / Mayans, O.
#1: Journal: Nature / Year: 1998
Title: Structural basis for activation of the titin kinase domain during myofibrillogenesis.
Authors: Mayans, O. / van der Ven, P.F. / Wilm, M. / Mues, A. / Young, P. / Furst, D.O. / Wilmanns, M. / Gautel, M.
#2: Journal: J.Synchrotron Radia. / Year: 1999
Title: X-ray analysis of protein crystals with thin-plate morphology
Authors: Mayans, O. / Wilmanns, M.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Titin
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0414
Polymers74,8562
Non-polymers1842
Water8,449469
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)37,4281
Polymers37,4281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6123
Polymers37,4281
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.860, 89.730, 113.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 37428.219 Da / Num. of mol.: 2 / Fragment: titin kinase: unp residues 32172-32492
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.06→28.979 Å / Num. obs: 49576 / % possible obs: 97.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.9
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.6 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TKI

1tki


Resolution: 2.06→28.979 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 1488 3 %FREERFLAG
Rwork0.1663 ---
obs0.1674 49576 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→28.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 12 469 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075348
X-RAY DIFFRACTIONf_angle_d17207
X-RAY DIFFRACTIONf_dihedral_angle_d15.1522023
X-RAY DIFFRACTIONf_chiral_restr0.072816
X-RAY DIFFRACTIONf_plane_restr0.003910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.12650.25851320.20834266X-RAY DIFFRACTION97
2.1265-2.20250.22861360.18914381X-RAY DIFFRACTION99
2.2025-2.29060.23141340.17524371X-RAY DIFFRACTION99
2.2906-2.39480.22531350.17244375X-RAY DIFFRACTION99
2.3948-2.5210.23621360.17624391X-RAY DIFFRACTION99
2.521-2.67880.23341360.17584359X-RAY DIFFRACTION99
2.6788-2.88550.21361350.17494384X-RAY DIFFRACTION98
2.8855-3.17560.20991350.1774351X-RAY DIFFRACTION98
3.1756-3.63430.20131340.16284368X-RAY DIFFRACTION97
3.6343-4.57590.17871370.13514379X-RAY DIFFRACTION97
4.5759-28.98190.15971380.16074463X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9140.45860.65290.5991-0.01651.457-0.0328-0.43660.01840.0967-0.02090.00350.0268-0.1350.01080.08210.0080.01380.0196-0.01550.017617.3915-2.4815-7.1488
23.1690.3096-0.68740.55370.05840.7149-0.0056-0.25870.07690.04730.00160.04750.0140.0456-0.00340.0792-0.0001-0.00890.0771-0.00280.045422.028-42.0517-27.9689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 338 )
2X-RAY DIFFRACTION2chain 'B' and (resid 18 through 338 )

+
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