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- PDB-4o00: Crystal structure of the Titin A-band domain A3 -

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Basic information

Entry
Database: PDB / ID: 4o00
TitleCrystal structure of the Titin A-band domain A3
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / beta barrel / fibronectin-3 domain / myosin-binding
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.853 Å
AuthorsRees, M.J. / Gautel, M.
CitationJournal: To be Published
Title: Crystal structure of the Titin A-band domain A3
Authors: Gautel, M. / Rees, M.J.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Titin
B: Titin


Theoretical massNumber of molelcules
Total (without water)23,0182
Polymers23,0182
Non-polymers00
Water6,035335
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)11,5091
Polymers11,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin


Theoretical massNumber of molelcules
Total (without water)11,5091
Polymers11,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.349, 63.447, 65.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA6792 - 6893
211chain BB6792 - 6895

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Components

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


Mass: 11508.903 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M SPG buffer, 0.01M Tris-HCl, 31% PEG1500, 50mM NaCl, 1mM DTT, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.541 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.85→21.15 Å / Num. all: 16016 / Num. obs: 15827 / % possible obs: 98.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.853-1.969194
3.362-20.7031100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrysalisProPROdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LPW RESIDUES 99-197

3lpw


Resolution: 1.853→20.702 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.18 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 788 4.99 %
Rwork0.1667 --
obs0.1687 15789 98.82 %
all-16016 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.715 Å2
Refinement stepCycle: LAST / Resolution: 1.853→20.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 0 335 1928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031647
X-RAY DIFFRACTIONf_angle_d0.8332242
X-RAY DIFFRACTIONf_dihedral_angle_d11.831644
X-RAY DIFFRACTIONf_chiral_restr0.033246
X-RAY DIFFRACTIONf_plane_restr0.004297
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A922X-RAY DIFFRACTION5.691TORSIONAL
12B922X-RAY DIFFRACTION5.691TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8525-1.96850.26631330.22182343X-RAY DIFFRACTION94
1.9685-2.12030.22211300.1842451X-RAY DIFFRACTION99
2.1203-2.33340.23411310.16312488X-RAY DIFFRACTION100
2.3334-2.67050.20211340.17442496X-RAY DIFFRACTION100
2.6705-3.36220.18991320.16212556X-RAY DIFFRACTION100
3.3622-20.70330.18621280.14722667X-RAY DIFFRACTION100
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)
15.4248-0.2131.89373.955-0.70446.4659-0.1053-0.46620.38150.3421-0.2022-0.311-0.23060.27-0.05270.126-0.02710.04390.0720.02540.1086-73.408875.49855.3782
22.91870.64430.55131.92540.07660.89680.00620.2014-0.163-0.21190.0313-0.14610.02320.0989-0.04060.07980.00450.02170.056-0.0110.06-81.288567.7796-2.8301
34.3062-2.77361.70183.2217-1.50110.8322-0.0745-0.4495-0.36010.21790.20960.5602-0.1577-0.1721-0.05540.11660.05390.0030.12060.00930.1212-94.282373.49274.5212
41.31070.00510.25383.0186-0.63492.5719-0.1260.014-0.13130.10880.03170.01780.0838-0.0707-0.03140.0506-0.0076-0.00550.05150.00550.0709-84.926263.75943.9477
51.4935-0.18980.29682.11420.16652.0378-0.0273-0.0797-0.0947-0.1819-0.02770.3511-0.0349-0.2477-0.00620.08130.0097-0.00080.0508-0.00030.1083-92.107668.81050.693
63.14320.0721.55472.15470.16452.8768-0.07430.07920.30230.0228-0.05370.0443-0.18680.17510.04620.0748-0.00510.03780.0502-0.0110.0398-84.064774.52221.6845
72.23231.23140.85880.72640.82612.9137-0.06440.7394-0.0143-0.165-0.03230.03780.028-0.5462-0.68680.2190.0422-0.33260.3228-0.02730.3392-100.31765.5254-12.842
84.25510.7543-1.66221.4732-1.09071.47030.0726-0.1328-0.12060.0497-0.1063-0.0222-0.04650.10660.01070.0769-0.0055-0.00410.0625-0.01210.0155-79.466445.20179.4667
92.35980.2449-0.43820.30340.22111.1962-0.1798-0.1985-0.1172-0.07590.0188-0.100900.2779-0.16090.0381-0.0045-0.01690.09110.01710.0536-71.691847.883710.6866
104.52491.60382.88542.07891.25573.5273-0.0261-0.35660.30140.1267-0.24020.2017-0.0689-0.3080.03050.0793-0.0059-0.00150.07110.01260.0856-88.032353.06218.8083
111.48551.029-0.35562.1063-0.29290.11110.0751-0.22650.06420.2433-0.038-0.1083-0.10420.08870.0950.0711-0.0072-0.00230.14780.01240.0974-78.597748.549917.8896
120.7789-0.03080.07871.3804-0.48851.5966-0.2342-0.06350.20730.08940.24940.2219-0.2232-0.4143-0.04850.0346-0.00880.00250.0549-0.00290.0798-88.00547.985810.0154
133.79932.18220.31323.2276-0.14891.6784-0.08670.4160.0947-0.22930.2272-0.4751-0.10390.010.06990.0516-0.01020.00250.04510.00540.1279-73.894254.3954.8652
141.3280.6766-0.12170.3648-0.10280.5567-0.02890.0377-0.05070.02130.08430.08610.0404-0.32010.05040.0797-0.0251-0.01270.13370.02450.1185-93.04236.739810.6017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 84 )
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 99 )
7X-RAY DIFFRACTION7chain 'A' and (resid 100 through 104 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 21 )
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 40 )
10X-RAY DIFFRACTION10chain 'B' and (resid 41 through 57 )
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 67 )
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 84 )
13X-RAY DIFFRACTION13chain 'B' and (resid 85 through 93 )
14X-RAY DIFFRACTION14chain 'B' and (resid 94 through 106 )

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