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- PDB-2j8h: Structure of the immunoglobulin tandem repeat A168-A169 of titin -

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Basic information

Entry
Database: PDB / ID: 2j8h
TitleStructure of the immunoglobulin tandem repeat A168-A169 of titin
ComponentsTITIN
KeywordsTRANSFERASE / CARDIOMYOPATHY / NUCLEAR PROTEIN / SERINE/THREONINE-PROTEIN KINASE / LIMB-GIRDLE MUSCULAR DYSTROPHY / PHOSPHORYLATION / DISEASE MUTATION / STRUCTURAL PROTEIN / TITIN / A-BAND / KINASE / WD REPEAT / TPR REPEAT / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN LIKE DOMAIN / NUCLEOTIDE-BINDING / ATP-BINDING / KELCH REPEAT
Function / homology
Function and homology information


sarcomerogenesis / 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 tissue morphogenesis / cardiac muscle hypertrophy / cardiac muscle cell development ...sarcomerogenesis / 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 tissue morphogenesis / cardiac muscle hypertrophy / cardiac muscle cell development / protein kinase regulator activity / mitotic chromosome condensation / Striated Muscle Contraction / muscle filament sliding / actinin binding / sarcomere organization / M band / positive regulation of cAMP/PKA signal transduction / I band / structural constituent of muscle / striated muscle thin filament / skeletal muscle thin filament assembly / cardiac muscle contraction / skeletal muscle contraction / muscle contraction / condensed nuclear chromosome / striated muscle contraction / response to calcium ion / Z disc / actin filament binding / actin cytoskeleton / Platelet degranulation / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / calcium ion binding / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / 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 V-Type / Immunoglobulin subtype 2 / Immunoglobulin C-2 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 / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 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 25, 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 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8582
Polymers21,7661
Non-polymers921
Water3,153175
1
A: TITIN
hetero molecules

A: TITIN
hetero molecules

A: TITIN
hetero molecules

A: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4328
Polymers87,0634
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area8530 Å2
ΔGint-38.9 kcal/mol
Surface area45380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)69.584, 87.040, 104.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein TITIN / CONNECTIN


Mass: 21765.820 Da / Num. of mol.: 1 / 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) / Strain (production host): BL21(DE3)
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCARDIAC TITIN IS THE ISOFORM 3 OF TITIN: UNP ENTRY Q8WZ42-3

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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: 3.3 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 9 / Details: AMMONIUM SULFATE, BICINE, pH 9

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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: 1.99→25 Å / Num. obs: 21381 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.7
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.99→67.42 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.331 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1088 5.1 %RANDOM
Rwork0.193 ---
obs0.194 20293 95.7 %-
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: 37.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---0.29 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.99→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 6 175 1706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221562
X-RAY DIFFRACTIONr_bond_other_d0.0010.021063
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9522115
X-RAY DIFFRACTIONr_angle_other_deg0.78132598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8895194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31924.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7915268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.613159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
X-RAY DIFFRACTIONr_nbd_refined0.20.2223
X-RAY DIFFRACTIONr_nbd_other0.20.21035
X-RAY DIFFRACTIONr_nbtor_refined0.180.2745
X-RAY DIFFRACTIONr_nbtor_other0.0860.2917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0121.51238
X-RAY DIFFRACTIONr_mcbond_other0.1541.5397
X-RAY DIFFRACTIONr_mcangle_it1.22521568
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1353690
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9324.5547
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
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 76 -
Rwork0.233 1453 -
obs--94.67 %
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)
13.9230.92491.53783.5512-0.04025.5941-0.10590.2234-0.163-0.06790.131-0.14030.14570.1177-0.0251-0.2110.0215-0.0312-0.174-0.0638-0.144315.96554.14614.324
22.66060.24820.20523.1821-1.67214.21410.15650.1542-0.0412-0.1412-0.064-0.09850.08480.0092-0.0924-0.1653-0.0670.0239-0.11880.0083-0.13996.380355.4294-26.1061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 95
2X-RAY DIFFRACTION2A96 - 195

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