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- PDB-1ya5: Crystal structure of the titin domains z1z2 in complex with telethonin -

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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


cardiac muscle cell development => GO:0055013 / FATZ binding / titin Z domain binding / BMP binding / protein serine/threonine kinase activity => GO:0004674 / otic vesicle formation / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly ...cardiac muscle cell development => GO:0055013 / FATZ binding / titin Z domain binding / BMP binding / protein serine/threonine kinase activity => GO:0004674 / otic vesicle formation / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / platelet degranulation / cardiac myofibril assembly / detection of mechanical stimulus / muscle filament sliding / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / adult heart development / cardiac muscle hypertrophy in response to stress / 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 / skeletal muscle contraction / striated muscle contraction / somitogenesis / protein kinase A signaling / titin binding / cardiac muscle contraction / response to muscle stretch / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / protein-macromolecule adaptor activity / Platelet degranulation / protein-containing complex assembly / protein tyrosine kinase activity / protease binding / transmembrane transporter binding / molecular adaptor activity / 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
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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