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- PDB-3qp3: Crystal structure of titin domain M4, tetragonal form -

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Basic information

Entry
Database: PDB / ID: 3qp3
TitleCrystal structure of titin domain M4, tetragonal form
ComponentsTitin
KeywordsTRANSFERASE / I-set Ig-like / sarcomere / M-band
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 / SAD / Resolution: 1.997 Å
AuthorsSauer, F. / Kolodziejczyk, A. / Wilmanns, M.
CitationJournal: To be Published
Title: Crystal structure of titin domain M4, tetragonal form
Authors: Sauer, F. / Kolodziejczyk, A. / Wilmanns, M.
History
DepositionFeb 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: Titin
B: Titin
C: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,32210
Polymers34,6493
Non-polymers6727
Water5,242291
1
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0306
Polymers11,5501
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6462
Polymers11,5501
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6462
Polymers11,5501
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.494, 63.494, 151.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 11549.802 Da / Num. of mol.: 3 / Fragment: domain M4 (UNP RESIDUES 33294-33395)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pETM-14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star pRARE2
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2M Na-citrate pH 4.0, 1.2M (NH4)2SO4, 0.3M MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.997→48.6 Å / Num. all: 21811 / Num. obs: 21724 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.15 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.5
Reflection shellResolution: 1.997→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3012 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.997→48.597 Å / SU ML: 0.25 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1100 5.08 %thin shells
Rwork0.177 ---
obs0.1789 21659 99.44 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.569 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.8907 Å2-0 Å20 Å2
2---0.8907 Å2-0 Å2
3---1.7814 Å2
Refinement stepCycle: LAST / Resolution: 1.997→48.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 35 291 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072392
X-RAY DIFFRACTIONf_angle_d1.0443273
X-RAY DIFFRACTIONf_dihedral_angle_d11.554832
X-RAY DIFFRACTIONf_chiral_restr0.073373
X-RAY DIFFRACTIONf_plane_restr0.004420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.997-2.08790.21941100.1985248798
2.0879-2.1980.22451650.18142501100
2.198-2.33570.22541100.17722554100
2.3357-2.51610.24081650.19282520100
2.5161-2.76920.2371100.18022594100
2.7692-3.16990.22661650.18052550100
3.1699-3.99340.19461100.1582655100
3.9934-48.61160.18971650.179269898
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)
11.03730.7165-0.72212.3775-0.23831.6439-0.0375-0.0641-0.65560.1618-0.0193-0.259-0.08390.45140.1780.0816-0.09360.02270.21120.01410.301715.64963.8339.8351
22.19591.41910.08441.2023-0.60551.5306-0.16540.54790.73120.19950.08440.1432-0.45250.31060.05440.238-0.07090.01760.13560.07980.2504-0.445316.03842.5739
32.8866-1.2970.40633.01370.36020.295-0.15430.1384-0.12120.1993-0.0593-0.0586-0.0720.04410.28710.1705-0.01470.02060.0961-0.0350.19995.37854.763914.7963
46.0541-1.7354-1.49090.98530.92420.92220.0040.6414-0.50990.0445-0.09950.10440.1623-0.20370.12260.1372-0.02180.02790.09110.00190.1343-2.23644.80657.4602
54.9112-0.92862.65040.7619-1.30182.5306-0.299-0.05650.52620.39980.1634-0.0083-0.5544-0.02860.19930.1546-0.0222-0.00590.01020.00410.19192.425313.357612.0912
61.16920.7267-0.00471.9080.33310.45940.0688-0.05770.03490.2079-0.03880.12780.0235-0.0439-0.02740.1032-0.01790.03290.057-0.00670.0844-28.575215.696221.0806
73.4731-1.1381.33271.9518-0.04950.61440.06970.49690.1086-0.0219-0.1284-0.02150.11010.15320.02170.1169-0.00820.01150.0930.00240.0462-26.26212.757815.5376
81.10791.7999-0.535.5035-1.35820.3899-0.22490.33690.3441-1.49960.09330.15040.30430.36080.17410.4412-0.0188-0.08140.24630.07930.1749-21.72769.127-5.4391
90.21080.0609-0.06860.4219-0.420.66320.22820.18250.0196-0.31620.06360.38960.1152-0.0318-0.27540.2608-0.0342-0.14520.08660.0240.2179-28.7708-12.39335.2784
101.16730.66270.28312.8006-0.89140.5250.0230.14540.1208-0.3520.03070.09560.17410.1089-0.06050.15830.00340.00750.06720.02480.0733-20.38654.44574.7898
110.77070.2084-0.60952.8637-1.0021.03930.08360.1095-0.0811-0.3828-0.1297-0.61530.40130.5933-0.05080.20420.01830.00160.16360.0140.1091-16.2011-3.93876.2044
122.0265-0.85380.24060.5077-0.44031.06120.10150.09710.0463-0.17520.04390.31480.0289-0.0904-0.10250.1119-0.0144-0.0150.04710.00420.0786-26.18530.06557.3397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:15)
2X-RAY DIFFRACTION2(chain A and resid 16:31)
3X-RAY DIFFRACTION3(chain A and resid 32:49)
4X-RAY DIFFRACTION4(chain A and resid 50:67)
5X-RAY DIFFRACTION5(chain A and resid 68:99)
6X-RAY DIFFRACTION6(chain B and resid 4:72)
7X-RAY DIFFRACTION7(chain B and resid 73:99)
8X-RAY DIFFRACTION8(chain C and resid 4:15)
9X-RAY DIFFRACTION9(chain C and resid 16:27)
10X-RAY DIFFRACTION10(chain C and resid 28:49)
11X-RAY DIFFRACTION11(chain C and resid 50:67)
12X-RAY DIFFRACTION12(chain C and resid 68:99)

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