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- PDB-3lpw: Crystal structure of the FnIII-tandem A77-A78 from the A-band of titin -

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Basic information

Entry
Database: PDB / ID: 3lpw
TitleCrystal structure of the FnIII-tandem A77-A78 from the A-band of titin
ComponentsA77-A78 domain from Titin
KeywordsSTRUCTURAL PROTEIN / intracellular FnIII-tandem
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBucher, R.M. / Mayans, O.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The structure of the FnIII Tandem A77-A78 points to a periodically conserved architecture in the myosin-binding region of titin
Authors: Bucher, R.M. / Svergun, D.I. / Muhle-Goll, C. / Mayans, O.
History
DepositionFeb 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: A77-A78 domain from Titin
B: A77-A78 domain from Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7135
Polymers43,3592
Non-polymers3553
Water12,520695
1
A: A77-A78 domain from Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9163
Polymers21,6791
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A77-A78 domain from Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7982
Polymers21,6791
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.900, 163.200, 65.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21A-247-

HOH

31A-486-

HOH

41A-660-

HOH

51B-419-

HOH

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Components

#1: Protein A77-A78 domain from Titin


Mass: 21679.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DL3)Rosetta / References: UniProt: Q8WZ42
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 3.56 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: Osmic confocal system
RadiationMonochromator: Cu-Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→19.805 Å / Num. obs: 74213 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.47 Å2 / Rsym value: 0.071 / Net I/σ(I): 11.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3775 / Rsym value: 0.368 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A170 extracted from PDB entry 2NZI

2nzi


Resolution: 1.65→19.805 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.858 / SU ML: 0.18 / Cross valid method: Free-R Flag, throughout / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 978 1.32 %FREERFLAG (CCP4) random selection
Rwork0.1789 ---
obs0.1793 74213 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.264 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 132.13 Å2 / Biso mean: 24.815 Å2 / Biso min: 4.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.606 Å20 Å2-0 Å2
2--2.069 Å20 Å2
3----0.464 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 24 695 3752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063159
X-RAY DIFFRACTIONf_angle_d1.0194306
X-RAY DIFFRACTIONf_dihedral_angle_d16.6151192
X-RAY DIFFRACTIONf_chiral_restr0.069493
X-RAY DIFFRACTIONf_plane_restr0.005549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.7370.3271180.309102761039498.76
1.737-1.8460.2491510.247104111056299.94
1.846-1.9880.2111200.191104261054699.94
1.988-2.1880.1821590.162104091056899.92
2.188-2.5040.2051400.164104691060999.71
2.504-3.1530.2071170.169105301064799.73
3.153-19.8060.1921730.154107141088799.11
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)
10.97390.4305-0.62721.6671-1.00880.91760.0238-0.08320.01680.0809-0.0742-0.0723-0.07940.05650.03050.1196-0.0578-0.01420.09770.01860.115646.481854.333729.7654
21.65910.32080.32570.3879-0.1240.994-0.14640.08690.2206-0.0790.05180.0628-0.1952-0.08980.09590.15-0.0048-0.0130.03610.02550.086949.447691.244210.3047
31.9420.1645-1.16331.2358-0.37870.88280.01530.0155-0.0072-0.0783-0.0357-0.00710.0972-0.01660.01050.0891-0.0587-0.00640.1520.01770.080630.748831.2185-14.2395
41.22430.0754-0.83451.28350.10612.0939-0.0424-0.1965-0.02710.0306-0.0007-0.09050.12810.07310.0460.05-0.0031-0.00190.1221-0.00280.053666.864733.23565.9789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:100A1 - 100
2X-RAY DIFFRACTION2chain A and resid 101:197A101 - 197
3X-RAY DIFFRACTION3chain B and resid 198:295B198 - 295
4X-RAY DIFFRACTION4chain B and resid 296:392B296 - 392

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