[English] 日本語
Yorodumi
- PDB-2j8o: Structure of the immunoglobulin tandem repeat of titin A168-A169 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j8o
TitleStructure of the immunoglobulin tandem repeat of titin A168-A169
ComponentsTITIN
KeywordsSTRUCTURAL PROTEIN / CARDIOMYOPATHY / NUCLEAR PROTEIN / SERINE/THREONINE-PROTEIN KINASE / LIMB-GIRDLE MUSCULAR DYSTROPHY / PHOSPHORYLATION / DISEASE MUTATION / TITIN / A-BAND / KINASE / WD REPEAT / TPR REPEAT / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN LIKE DOMAIN / NUCLEOTIDE-BINDING / ATP-BINDING / TRANSFERASE / KELCH REPEAT
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / detection of muscle stretch / muscle alpha-actinin binding / protein kinase A signaling / cardiac myofibril assembly / cardiac muscle hypertrophy ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / detection of muscle stretch / muscle alpha-actinin binding / protein kinase A signaling / 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 / Z disc / response to calcium ion / 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 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-Type / 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 / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / 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: 2.49 Å
AuthorsMueller, S. / Lange, S. / Kursula, I. / Gautel, M. / Wilmanns, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Rigid Conformation of an Immunoglobulin Domain Tandem Repeat in the A-Band of the Elastic Muscle Protein Titin
Authors: Mueller, S. / Lange, S. / Gautel, M. / Wilmanns, M.
History
DepositionOct 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TITIN
B: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7164
Polymers43,5322
Non-polymers1842
Water82946
1
A: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8582
Polymers21,7661
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8582
Polymers21,7661
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.560, 122.487, 98.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEALAALAAA5 - 907 - 92
21PHEPHEALAALABB5 - 907 - 92
12ILEILEGLUGLUAA100 - 190102 - 192
22ILEILEGLUGLUBB100 - 190102 - 192

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.9905, 0.1369, -0.01166), (0.137, 0.9906, -0.005752), (0.01076, -0.007295, -0.9999)
Vector: 139.3, -9.267, 52.97)

-
Components

#1: Protein TITIN / CONNECTIN


Mass: 21765.820 Da / Num. of mol.: 2 / Fragment: IG LIKE DOMAIN, RESIDUES 24430-24623
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Organ: HEART / Plasmid: PETM11 / 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.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINUS CHANGED FROM Q (ORIGINAL) TO GAMA DUE TO CLONING. CARDIAC TITIN IS Q8WZ42 ISOFORM 3.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 9 / Details: AMMONIUM SULFATE, BICINE, pH 9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 3, 2003 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 2.48→25 Å / Num. obs: 20714 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 43.1
Reflection shellResolution: 2.48→2.57 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8H

2j8h


Resolution: 2.49→100 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 25.481 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1065 5.1 %RANDOM
Rwork0.249 ---
obs0.252 19645 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.38 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å20 Å2
2--4.1 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.49→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 12 46 3105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223121
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9524226
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3775388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11124.245139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7631518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022352
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.21239
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22060
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.51982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91923135
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41231280
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.24.51091
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1344medium positional0.220.5
2364medium positional0.290.5
1336loose positional0.655
2347loose positional0.765
1344medium thermal0.72
2364medium thermal1.162
1336loose thermal1.7810
2347loose thermal1.7710
LS refinement shellResolution: 2.48→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 91 -
Rwork0.344 1400 -
obs--97.32 %
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)
12.7351-0.1119-0.43854.7821.54954.3002-0.06870.15680.0383-0.0083-0.17250.2557-0.2169-0.15930.2412-0.1026-0.00830.0713-0.16-0.1487-0.001562.61547.49241.092
24.51820.4453-0.62574.25332.335210.14670.00190.98930.4985-0.2915-0.1411-0.1474-0.722-1.25580.1392-0.22830.2633-0.08590.63210.0188-0.387160.13637.9940.752
34.9975-0.28050.91235.78020.818113.3587-0.09040.84550.7728-0.2904-0.1743-0.2356-1.57171.00590.2646-0.0012-0.068-0.0060.17720.2682-0.057883.37545.8212.42
47.071-0.69610.19986.9159-0.58116.2629-0.1385-1.04810.23550.59810.151-0.2384-0.20280.2008-0.0125-0.23080.0317-0.0495-0.0616-0.0485-0.165784.5336.07653.199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 95
2X-RAY DIFFRACTION2A96 - 194
3X-RAY DIFFRACTION3B1 - 95
4X-RAY DIFFRACTION4B96 - 195

+
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