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- PDB-6h4l: Structure of Titin M4 trigonal form -

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Basic information

Entry
Database: PDB / ID: 6h4l
TitleStructure of Titin M4 trigonal form
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / Titin / Muscle / Sarcomere / Ig-like
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / 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 / striated muscle contraction / protein kinase A signaling / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / 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
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: 1.6 Å
AuthorsSauer, F. / Wilmanns, M.
CitationJournal: Plos One / Year: 2019
Title: Structural diversity in the atomic resolution 3D fingerprint of the titin M-band segment.
Authors: Chatziefthimiou, S.D. / Hornburg, P. / Sauer, F. / Mueller, S. / Ugurlar, D. / Xu, E.R. / Wilmanns, M.
History
DepositionJul 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7225
Polymers11,5501
Non-polymers1724
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-56 kcal/mol
Surface area5680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.847, 84.847, 49.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

21A-417-

HOH

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Components

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


Mass: 11549.802 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 4.42 Å3/Da / Density % sol: 72.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES pH 6.5 2M RbBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.286 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.286 Å / Relative weight: 1
ReflectionResolution: 1.6→42.4 Å / Num. obs: 27114 / % possible obs: 99.6 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Net I/σ(I): 24.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.458 / Num. unique obs: 3942 / Rpim(I) all: 0.203 / Rsym value: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.773 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2212 1740 6.43 %
Rwork0.208 --
obs0.2089 27076 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 4 195 951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006786
X-RAY DIFFRACTIONf_angle_d1.0811073
X-RAY DIFFRACTIONf_dihedral_angle_d13.41284
X-RAY DIFFRACTIONf_chiral_restr0.475126
X-RAY DIFFRACTIONf_plane_restr0.004137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64710.23111430.24942090X-RAY DIFFRACTION100
1.6471-1.70020.26011440.23022115X-RAY DIFFRACTION100
1.7002-1.7610.25591420.21622070X-RAY DIFFRACTION100
1.761-1.83150.26461430.22832109X-RAY DIFFRACTION100
1.8315-1.91480.21291460.2052109X-RAY DIFFRACTION100
1.9148-2.01580.23321470.19332091X-RAY DIFFRACTION100
2.0158-2.1420.20321480.19472110X-RAY DIFFRACTION100
2.142-2.30730.21151450.20862101X-RAY DIFFRACTION100
2.3073-2.53940.25151440.21462138X-RAY DIFFRACTION100
2.5394-2.90650.26021440.21392138X-RAY DIFFRACTION100
2.9065-3.66050.20891460.19882149X-RAY DIFFRACTION100
3.6605-27.77680.21480.20882116X-RAY DIFFRACTION95
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)
12.3836-1.0531-0.27024.12471.60914.3256-0.02190.06670.02140.050.2763-0.22980.46490.125-0.13660.24480.0047-0.01650.086-0.02040.1873-40.55886.58438.3236
23.22820.25710.14634.43681.03482.5233-0.07040.5210.2984-0.79970.1120.4792-0.1186-0.1165-0.11270.3116-0.0281-0.05630.22340.03980.2131-45.862411.6465-1.2326
32.3732-0.4361-0.09131.8770.17181.5301-0.04030.52030.23-0.56760.2656-0.06980.0541-0.144-0.03130.3109-0.03840.03510.1311-0.00190.1585-41.70969.45690.9463
45.2264-3.2393-2.96436.4344.64093.70540.31160.42820.2753-0.78180.2994-0.8724-0.54840.0607-0.61140.3335-0.02010.09590.1964-0.04720.3032-34.11589.65171.0041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 99 )

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