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- PDB-5jdj: Crystal structure of domain I10 from titin in space group P212121 -

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Basic information

Entry
Database: PDB / ID: 5jdj
TitleCrystal structure of domain I10 from titin in space group P212121
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / titin / muscle
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / 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 hypertrophy ...sarcomerogenesis / titin-telethonin complex / 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 hypertrophy / mitotic chromosome condensation / protein kinase regulator activity / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / 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 / response to calcium ion / Z disc / 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 / 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: 1.738 Å
AuthorsWilliams, R. / Bogomolovas, J. / Labiet, S. / Mayans, O.
CitationJournal: Open Biology / Year: 2016
Title: Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I.
Authors: Bogomolovas, J. / Fleming, J.R. / Anderson, B.R. / Williams, R. / Lange, S. / Simon, B. / Khan, M.M. / Rudolf, R. / Franke, B. / Bullard, B. / Rigden, D.J. / Granzier, H. / Labeit, S. / Mayans, O.
History
DepositionApr 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 12, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin
B: Titin
C: Titin
D: Titin
E: Titin
F: Titin
G: Titin
H: Titin
I: Titin
J: Titin
K: Titin
L: Titin
M: Titin
N: Titin
O: Titin
P: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,09822
Polymers162,85816
Non-polymers2406
Water29,7611652
1
A: Titin
L: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4374
Polymers20,3572
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin
P: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4374
Polymers20,3572
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Titin
M: Titin


Theoretical massNumber of molelcules
Total (without water)20,3572
Polymers20,3572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Titin
E: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3973
Polymers20,3572
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Titin
N: Titin


Theoretical massNumber of molelcules
Total (without water)20,3572
Polymers20,3572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: Titin
J: Titin


Theoretical massNumber of molelcules
Total (without water)20,3572
Polymers20,3572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
H: Titin
I: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3973
Polymers20,3572
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
K: Titin
O: Titin


Theoretical massNumber of molelcules
Total (without water)20,3572
Polymers20,3572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.637, 136.239, 140.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 10178.617 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1652 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M CaCl2, 0.1 M Tris pH 7.5, 25% [w/v] PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.738→29.652 Å / Num. obs: 145378 / % possible obs: 98.77 % / Redundancy: 7.5 % / Rsym value: 0.096 / Net I/σ(I): 15.38
Reflection shellResolution: 1.738→1.8 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.77 / Num. unique all: 13857 / Rsym value: 0.714 / % possible all: 95.19

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.738→29.652 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 1455 1 %
Rwork0.186 --
obs0.1864 145370 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.738→29.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11112 0 6 1652 12770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811395
X-RAY DIFFRACTIONf_angle_d1.11515464
X-RAY DIFFRACTIONf_dihedral_angle_d13.9514173
X-RAY DIFFRACTIONf_chiral_restr0.0441885
X-RAY DIFFRACTIONf_plane_restr0.0051940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7379-1.80.32041370.271713719X-RAY DIFFRACTION95
1.8-1.87210.26431540.22514300X-RAY DIFFRACTION99
1.8721-1.95730.2561400.202314303X-RAY DIFFRACTION99
1.9573-2.06040.25131200.202714205X-RAY DIFFRACTION98
2.0604-2.18950.23631560.192414401X-RAY DIFFRACTION100
2.1895-2.35850.28591370.192414460X-RAY DIFFRACTION100
2.3585-2.59570.2381570.196114493X-RAY DIFFRACTION100
2.5957-2.9710.22371480.190814382X-RAY DIFFRACTION98
2.971-3.7420.21781430.162314677X-RAY DIFFRACTION100
3.742-29.65620.17141630.167714975X-RAY DIFFRACTION99

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