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- PDB-2y9r: Crystal structure of the M10 domain of Titin -

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Basic information

Entry
Database: PDB / ID: 2y9r
TitleCrystal structure of the M10 domain of Titin
ComponentsTITIN
KeywordsTRANSFERASE / SARCOMERE / M-BAND / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / actinin binding / M band / 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 / striated muscle contraction / cardiac muscle contraction / protein kinase A signaling / condensed nuclear chromosome / muscle contraction / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / 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
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 / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A.
Citation
Journal: To be Published
Title: Crystal Structure of the Titin M10 Domain
Authors: Pernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Insight Into M-Band Assembly and Mechanics from the Titin-Obscurin-Like-1 Complex.
Authors: Pernigo, S. / Fukuzawa, A. / Bertz, M. / Holt, M. / Rief, M. / Steiner, R.A. / Gautel, M.
History
DepositionFeb 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0753
Polymers10,9811
Non-polymers1,0932
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.450, 43.450, 56.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11T-2007-

HOH

21T-2009-

HOH

31T-2028-

HOH

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Components

#1: Protein TITIN / CONNECTIN / RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.14


Mass: 10981.231 Da / Num. of mol.: 1 / Fragment: M10 DOMAIN, RESIDUES 26828-26926
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Description: CHAIN T OF 2WP3 WAS USED FOR MOLECULAR REPLACEMENT
Crystal growpH: 6.5 / Details: 35% PEG 400, 0.1M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9704
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 4, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9704 Å / Relative weight: 1
ReflectionResolution: 1.9→34.42 Å / Num. obs: 8350 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0101refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WP3

2wp3


Resolution: 1.9→34.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.802 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS AT RIDING POSITIONS HAVE BEEN USED IN REFINEMENT. N-TERMINAL GLY-SER-SER RESIDUES FROM THE VECTOR AND C-TERMINAL ILE ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24108 406 4.9 %RANDOM
Rwork0.19361 ---
obs0.19592 7929 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 0 25 44 814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022803
X-RAY DIFFRACTIONr_bond_other_d0.0020.02545
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.981087
X-RAY DIFFRACTIONr_angle_other_deg0.80231348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80625.15233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9315133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.323154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 34 -
Rwork0.26 559 -
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)
19.0088-11.9449-3.389916.0545.58247.3443-0.04650.2694-0.41580.2258-0.46890.60340.6828-0.53040.51540.1565-0.12120.01840.1031-0.01670.0473-3.8766-24.4502-7.2126
23.0456-0.00210.85236.10114.09593.2480.49480.64840.169-0.185-0.2602-0.84590.0374-0.1387-0.23460.13310.07060.06010.2319-0.05310.4122-1.0805-10.04282.353
310.1655-18.2062.012147.5162.99976.58370.3367-0.46390.23290.441-0.3163-0.2204-0.3903-0.255-0.02040.3389-0.19210.06420.1479-0.04660.0391-4.24255.19138.6937
41.911-2.81851.14529.67315.77825.4470.00970.2420.18130.0560.2302-0.5980.0420.3017-0.23990.0331-0.02510.03710.0818-0.00860.0956-5.46965.61891.4535
54.84885.60871.731632.26162.5040.6472-0.1469-0.09890.0062-0.68490.2114-1.0201-0.0986-0.0021-0.06450.1166-0.04640.09160.0648-0.06490.1269-3.3261-14.7464-6.9217
66.4704-12.5452-10.925424.35921.531822.05860.13270.2023-0.4183-0.2347-0.43040.77090.1607-0.69910.29770.1307-0.0007-0.05980.07340.01220.0814-10.8445-15.5762-7.862
721.00393.6565-2.578710.4883-3.121710.36150.2345-0.60220.32160.391-0.09720.7712-0.1485-0.7771-0.13730.05060.012-0.00020.102-0.03060.0822-17.5456-6.50173.0348
85.4059-1.1541-2.47569.09841.71091.2925-0.19660.72070.2967-0.59070.30050.368-0.0033-0.2621-0.10390.1141-0.018-0.04190.2002-0.02260.1676-18.3765-0.4355-4.8696
92.3354-2.37150.01139.77743.21074.48750.20630.30350.2975-0.2806-0.02250.1174-0.3076-0.3797-0.18370.08120.05890.05370.1670.08460.1387-15.824.641-3.4754
106.4579-1.9865-3.85847.64596.676713.19360.15930.21280.291-0.4495-0.0808-0.5067-0.2147-0.0093-0.07850.09930.00010.06640.10560.00730.0753-6.059-6.6456-9.2012
115.72180.3152-2.295425.967611.392815.0608-0.04490.53610.5496-0.74950.10490.0575-0.4271-0.1672-0.060.0251-0.0071-0.00380.09480.02950.071-10.5685.0206-0.9883
1211.0274-4.3304-3.735316.53063.547516.80880.45580.13930.65610.0335-0.23520.8484-0.5683-0.7913-0.22060.05620.00530.06080.0599-0.01430.1353-13.71467.5818.5667
130.8684-2.8584-2.47169.78928.46237.3240.0291-0.02730.04560.20440.0993-0.18160.17940.0597-0.12830.1848-0.0098-0.01250.0321-0.03420.0396-10.9943-9.58452.849
146.87268.484.415128.992628.712732.088-0.27460.1465-0.16310.0806-0.30480.38890.3536-0.53970.57930.0860.0033-0.00930.03670.00590.1142-9.5801-21.2302-2.9923
153.1184-1.79922.481718.38634.68395.29630.1237-0.16020.31780.93150.0041-1.0411-0.03150.1496-0.12780.2606-0.1387-0.00360.0916-0.03330.0805-6.06362.260410.9832
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 6
2X-RAY DIFFRACTION2T7 - 12
3X-RAY DIFFRACTION3T13 - 18
4X-RAY DIFFRACTION4T19 - 25
5X-RAY DIFFRACTION5T26 - 31
6X-RAY DIFFRACTION6T32 - 37
7X-RAY DIFFRACTION7T38 - 44
8X-RAY DIFFRACTION8T45 - 49
9X-RAY DIFFRACTION9T50 - 55
10X-RAY DIFFRACTION10T56 - 63
11X-RAY DIFFRACTION11T64 - 68
12X-RAY DIFFRACTION12T69 - 73
13X-RAY DIFFRACTION13T74 - 83
14X-RAY DIFFRACTION14T84 - 90
15X-RAY DIFFRACTION15T91 - 98

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