[English] 日本語
Yorodumi
- PDB-2f8v: Structure of full length telethonin in complex with the N-terminu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f8v
TitleStructure of full length telethonin in complex with the N-terminus of titin
Components
  • N2B-Titin Isoform
  • Telethonin
KeywordsCONTRACTILE PROTEIN/CONTRACTILE PROTEIN / Sarcomere / Titin / Z1Z2 / Telethonin / CONTRACTILE PROTEIN-CONTRACTILE PROTEIN COMPLEX
Function / homology
Function and homology information


FATZ binding / titin Z domain binding / otic vesicle formation / BMP binding / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch ...FATZ binding / titin Z domain binding / otic vesicle formation / BMP binding / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / detection of mechanical stimulus / muscle alpha-actinin binding / : / cardiac myofibril assembly / adult heart development / cardiac muscle hypertrophy / mitotic chromosome condensation / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / cardiac muscle hypertrophy in response to stress / 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 / somitogenesis / striated muscle contraction / cardiac muscle contraction / titin binding / response to muscle stretch / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / response to calcium ion / Z disc / actin filament binding / Platelet degranulation / protein-containing complex assembly / protease binding / protein tyrosine kinase activity / protein-macromolecule adaptor activity / molecular adaptor activity / transmembrane transporter binding / 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
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 / 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: 2.75 Å
AuthorsPinotsis, N. / Petoukhov, M. / Lange, S. / Svergun, D. / Zou, P. / Gautel, M. / Wilmanns, M.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: Evidence for a dimeric assembly of two titin/telethonin complexes induced by the telethonin C-terminus.
Authors: Pinotsis, N. / Petoukhov, M. / Lange, S. / Svergun, D. / Zou, P. / Gautel, M. / Wilmanns, M.
History
DepositionDec 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4Oct 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N2B-Titin Isoform
B: N2B-Titin Isoform
T: Telethonin
C: N2B-Titin Isoform
D: N2B-Titin Isoform
Y: Telethonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,79911
Polymers124,3196
Non-polymers4805
Water1,42379
1
A: N2B-Titin Isoform
B: N2B-Titin Isoform
T: Telethonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4476
Polymers62,1593
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-47 kcal/mol
Surface area23920 Å2
MethodPISA
2
C: N2B-Titin Isoform
D: N2B-Titin Isoform
Y: Telethonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3515
Polymers62,1593
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-40 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.513, 46.885, 128.033
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13B
23D
14B
24D
15T
25Y
16T
26Y
17T
27Y

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLUGLUAA4 - 1004 - 100
211GLNGLNGLUGLUCD4 - 1004 - 100
112THRTHRGLNGLNAA101 - 194101 - 194
212THRTHRGLNGLNCD101 - 194101 - 194
113THRTHRGLUGLUBB3 - 1003 - 100
213THRTHRGLUGLUDE3 - 1003 - 100
114THRTHRGLNGLNBB101 - 194101 - 194
214THRTHRGLNGLNDE101 - 194101 - 194
115SERSERPHEPHETC8 - 218 - 21
215SERSERPHEPHEYF8 - 218 - 21
116ARGARGGLNGLNTC33 - 5433 - 54
216ARGARGGLNGLNYF33 - 5433 - 54
117METMETSERSERTC1 - 71 - 7
217METMETSERSERYF1 - 71 - 7
127TRPTRPTHRTHRTC22 - 3222 - 32
227TRPTRPTHRTHRYF22 - 3222 - 32
137GLYGLYLEULEUTC55 - 8355 - 83
237GLYGLYLEULEUYF55 - 8355 - 83

NCS ensembles :
ID
1
2
3
4
5
6
7
DetailsThe biological assembly is the dimer in the asymmetric unit

-
Components

#1: Protein
N2B-Titin Isoform


Mass: 21582.982 Da / Num. of mol.: 4 / Fragment: Domains Z1Z2, residues 1-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WZ42
#2: Protein Telethonin / Titin cap protein


Mass: 18993.307 Da / Num. of mol.: 2 / Mutation: C8S, C15S, C38S, C57S, C127S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCAP / 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.: 79 / 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: 54.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.45
Details: PEG35000, LITHIUM SULPHATE, ACETATE BUFFER, 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 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2002
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8117 Å / Relative weight: 1
ReflectionResolution: 2.75→23.9 Å / Num. all: 33692 / Num. obs: 33692 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.101
Reflection shellResolution: 2.75→2.8 Å / % possible all: 79.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YA5

1ya5


Resolution: 2.75→23.9 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.879 / SU B: 30.486 / SU ML: 0.292 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.174 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28733 1063 3.2 %RANDOM
Rwork0.26671 ---
all0.2655 32562 --
obs0.26734 32562 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.944 Å2
Baniso -1Baniso -2Baniso -3
1-7.18 Å20 Å2-5.44 Å2
2---7.85 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.75→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 25 79 7384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227457
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.95710154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8255949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14224.36328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.342151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4581552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025652
X-RAY DIFFRACTIONr_nbd_refined0.2880.22983
X-RAY DIFFRACTIONr_nbtor_refined0.340.25048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4190.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.29
X-RAY DIFFRACTIONr_mcbond_it1.60454826
X-RAY DIFFRACTIONr_mcangle_it1.99667694
X-RAY DIFFRACTIONr_scbond_it2.61462904
X-RAY DIFFRACTIONr_scangle_it3.1037.52460
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A388medium positional0.180.5
2A376medium positional0.070.5
3B392medium positional0.060.5
4B372medium positional0.110.5
5C56medium positional0.040.5
6C88medium positional0.050.5
7C184medium positional0.110.5
1A327loose positional0.525
2A346loose positional0.135
3B330loose positional0.175
4B339loose positional0.195
5C60loose positional0.095
6C101loose positional0.075
7C174loose positional0.145
1A388medium thermal0.952
2A376medium thermal0.972
3B392medium thermal1.012
4B372medium thermal1.112
5C56medium thermal0.822
6C88medium thermal0.912
7C184medium thermal0.972
1A327loose thermal1.9710
2A346loose thermal1.6710
3B330loose thermal2.0510
4B339loose thermal2.1210
5C60loose thermal1.5310
6C101loose thermal1.6610
7C174loose thermal1.5410
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 65 -
Rwork0.358 1966 -
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)
14.1782-0.63084.28530.7602-1.32475.64140.0481-0.2782-0.0996-0.03530.12070.00250.276-0.3857-0.1687-0.2630.03630.0364-0.34050.0014-0.241723.37233.745946.8232
22.3713-0.29593.77731.07480.25797.4257-0.107-0.17650.02890.14480.0233-0.01020.0228-0.32270.0837-0.4288-0.06150.0796-0.32210.0424-0.257714.187759.290732.4648
35.0431-0.84587.22040.23-1.139210.39630.0882-0.3848-0.0390.10230.0816-0.02460.2667-0.627-0.1698-0.1854-0.0576-0.0274-0.24070.0363-0.120418.082648.563538.4097
40.77860.8161-0.78264.9633-4.98188.19330.06450.08120.14340.3879-0.0934-0.3209-1.183-0.06480.0289-0.03630.14030.26330.180.045-0.04553.717118.6503109.6767
51.4956-0.84921.51555.4061-7.09812.8136-0.2202-0.2984-0.21960.6524-0.1371-0.1932-0.59590.43930.3573-0.25720.0280.36590.19670.0392-0.0319.563520.168583.6137
61.5277-3.01493.65038.161-11.173115.84720.109-0.22-0.0686-0.06920.05560.0377-0.17170.1931-0.16460.27370.13610.24570.43690.00250.293512.890920.122894.3324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1952 - 195
2X-RAY DIFFRACTION2BB1 - 1971 - 197
3X-RAY DIFFRACTION3TC1 - 881 - 88
4X-RAY DIFFRACTION4CD4 - 1944 - 194
5X-RAY DIFFRACTION5DE2 - 1942 - 194
6X-RAY DIFFRACTION6YF1 - 881 - 88

+
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