[English] 日本語
Yorodumi
- PDB-1ya5: Crystal structure of the titin domains z1z2 in complex with telethonin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ya5
TitleCrystal structure of the titin domains z1z2 in complex with telethonin
Components
  • N2B-TITIN ISOFORM
  • TELETHONIN
KeywordsSTRUCTURAL PROTEIN / TELETHONIN / T-CAP / Ig-LIKE DOMAINS / Z1 / Z2 / TITIN
Function / homology
Function and homology information


otic vesicle formation / FATZ binding / titin Z domain binding / BMP binding / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of mechanical stimulus ...otic vesicle formation / FATZ binding / titin Z domain binding / BMP binding / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of mechanical stimulus / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / adult heart development / cardiac muscle hypertrophy in response to stress / protein kinase regulator activity / cardiac muscle hypertrophy / mitotic chromosome condensation / actinin binding / Striated Muscle Contraction / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle contraction / somitogenesis / cardiac muscle contraction / striated muscle contraction / titin binding / muscle contraction / protein kinase A signaling / response to muscle stretch / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / protein-macromolecule adaptor activity / protein tyrosine kinase activity / protein-containing complex assembly / protease binding / transmembrane transporter binding / molecular adaptor activity / non-specific serine/threonine protein kinase / calmodulin binding / 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
titin filament fold / titin domain like / Telethonin / Titin-like domain superfamily / Telethonin protein / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain ...titin filament fold / titin domain like / Telethonin / Titin-like domain superfamily / Telethonin protein / 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 / Single Sheet / 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 / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / 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
Telethonin / Titin / Titin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.445 Å
AuthorsPinotsis, N. / Popov, A. / Zou, P. / Wilmanns, M.
Citation
Journal: Nature / Year: 2006
Title: Palindromic assembly of the giant muscle protein titin in the sarcomeric Z-disk
Authors: Zou, P. / Pinotsis, N. / Lange, S. / Song, Y.H. / Popov, A. / Mavridis, I. / Mayans, O.M. / Gautel, M. / Wilmanns, M.
#1: Journal: Thesis / Year: 2003
Title: Crystal structure of the titin domains z1z2 in complex with telethonin
Authors: Pinotsis, N.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N2B-TITIN ISOFORM
B: N2B-TITIN ISOFORM
T: TELETHONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2668
Polymers53,7863
Non-polymers4805
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-77 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.326, 63.213, 242.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein N2B-TITIN ISOFORM / TTN protein / titin isoform novex-2 / titin isoform novex-1


Mass: 21582.982 Da / Num. of mol.: 2 / Fragment: domains Z1Z2, RESIDUES 1-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET6D (Modified PET3A) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PJP0, UniProt: Q8WZ42*PLUS
#2: Protein TELETHONIN / Titin cap protein


Mass: 10619.717 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-90 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: O15273
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.23 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.45
Details: pH 4.45, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8117
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 2001
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8117 Å / Relative weight: 1
ReflectionResolution: 2.445→14.92 Å / Num. obs: 25248 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.2
Reflection shellResolution: 2.445→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.1 / % possible all: 86.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MAD / Resolution: 2.445→14.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU B: 22.308 / SU ML: 0.239 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26496 812 3.2 %RANDOM
Rwork0.23173 ---
all0.23278 24382 --
obs0.23278 24382 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.547 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20 Å2
2--9.26 Å20 Å2
3----5.87 Å2
Refinement stepCycle: LAST / Resolution: 2.445→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 25 179 3910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223805
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9625182
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39124.458166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.05815622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1531526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022873
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2910.21788
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.22564
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3540.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.01752453
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.74163925
X-RAY DIFFRACTIONr_scbond_it4.40961479
X-RAY DIFFRACTIONr_scangle_it5.6087.51257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.445→2.507 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 44 -
Rwork0.355 1594 -
obs--100 %
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)
10.54950.0077-0.14981.1252-2.12916.7431-0.13280.01-0.05650.27050.075-0.0441-0.7208-0.61050.0578-0.09280.04040.0029-0.2291-0.0412-0.049415.111716.422453.7891
20.78190.1606-0.33540.65510.060712.25020.0338-0.0955-0.0240.05890.0176-0.0561-0.31140.9718-0.0514-0.20380.00920.0216-0.1972-0.02290.009140.25618.930636.1653
30.03050.0192-0.25330.541-0.72639.74250.0772-0.1735-0.04920.09870.0428-0.08190.1669-0.0083-0.12-0.10050.0065-0.0006-0.3096-0.04-0.007529.790117.721543.1079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1981 - 198
2X-RAY DIFFRACTION2BB1 - 1971 - 197
3X-RAY DIFFRACTION3TC1 - 891 - 89

+
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