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- PDB-3lcy: Titin Ig tandem domains A164-A165 -

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Basic information

Entry
Database: PDB / ID: 3lcy
TitleTitin Ig tandem domains A164-A165
ComponentsTitin
KeywordsTRANSFERASE / Titin / A-band / Ig tandem domains / ATP-binding / Calmodulin-binding / Cardiomyopathy / Disease mutation / Disulfide bond / Immunoglobulin domain / Isopeptide bond / Kelch repeat / Kinase / Limb-girdle muscular dystrophy / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / TPR repeat / WD repeat
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 / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / sarcomere organization / structural constituent of muscle / 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: 2.5 Å
AuthorsChen, Q. / Groves, M.R. / Wilmanns, M.
CitationJournal: To be Published
Title: Structural investigation of the Titin A-band tandem Ig domains A164-A165
Authors: Chen, Q. / Wilmanns, M.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin
B: Titin
C: Titin
D: Titin


Theoretical massNumber of molelcules
Total (without water)88,9944
Polymers88,9944
Non-polymers00
Water5,981332
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)22,2481
Polymers22,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin


Theoretical massNumber of molelcules
Total (without water)22,2481
Polymers22,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Titin


Theoretical massNumber of molelcules
Total (without water)22,2481
Polymers22,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Titin


Theoretical massNumber of molelcules
Total (without water)22,2481
Polymers22,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.086, 103.821, 116.533
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-IDDetails
11A
21B
12C
22B
13D
23B

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 4 - 197 / Label seq-ID: 4 - 197

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12CC
22BB
13DD
23BB

NCS ensembles :
ID
1
2
3
DetailsMonomer in solution as determined by static light scattering

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Components

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


Mass: 22248.428 Da / Num. of mol.: 4 / Fragment: Titin A-band tandem Ig domains A164-A165
Source method: isolated from a genetically manipulated source
Details: sarcomere / Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pETZ2_1a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes PH 7.5, 10% iso-propanol 8.5% PEG20,000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 12, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 2.5→43.06 Å / Num. all: 32998 / Num. obs: 32969 / % possible obs: 99.4 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.4 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIXdev_276refinement
SOLVEphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
DNAdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.5→36.59 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.866 / SU B: 22.367 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.581 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1666 5.1 %RANDOM
Rwork0.2035 ---
obs0.2035 31271 99.37 %-
all-48357 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 3.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å2-0 Å20 Å2
2--0.27 Å2-0 Å2
3----1.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.4116 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6210 0 0 332 6542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0180.0226309
X-RAY DIFFRACTIONf_bond_other_d
X-RAY DIFFRACTIONf_angle_refined_deg1.6361.968523
X-RAY DIFFRACTIONf_angle_other_deg
X-RAY DIFFRACTIONf_dihedral_angle_1_deg7.1445775
X-RAY DIFFRACTIONf_dihedral_angle_2_deg33.86424.571280
X-RAY DIFFRACTIONf_dihedral_angle_3_deg19.533151166
X-RAY DIFFRACTIONf_dihedral_angle_4_deg18.8291532
X-RAY DIFFRACTIONf_chiral_restr0.1040.2951
X-RAY DIFFRACTIONf_gen_planes_refined0.0060.0214676
X-RAY DIFFRACTIONf_gen_planes_other
X-RAY DIFFRACTIONf_nbd_refined
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it0.3421.53863
X-RAY DIFFRACTIONf_mcbond_other
X-RAY DIFFRACTIONf_mcangle_it0.6226265
X-RAY DIFFRACTIONf_scbond_it1.32432446
X-RAY DIFFRACTIONf_scangle_it2.1974.52258
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A772tight positional0.130.05
2C776tight positional0.180.05
3D776tight positional0.160.05
1A764medium positional0.320.5
2C766medium positional0.310.5
3D766medium positional0.330.5
1A772tight thermal0.490.5
2C776tight thermal0.280.5
3D776tight thermal0.80.5
1A764medium thermal0.642
2C766medium thermal0.412
3D766medium thermal0.932
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 112 -
Rwork0.286 2103 -
obs--91.87 %
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)
125.9291-2.40889.5365-0.5528-1.36854.1592-1.4901-0.04261.9145-0.06380.0681-0.32990.27080.10771.4220.41080.02370.26360.6026-0.38431.17253.970127.0688-29.478
257.44239.25843.26965.2873.09491.346-0.7827-1.3216-1.03590.17620.7469-0.81030.62880.28790.03580.5884-0.20160.42360.6116-0.43830.8924-11.180424.2622-25.1913
36.46780.02350.06971.6170.30760.8496-0.26360.00270.4683-0.14220.1591-0.2418-0.17050.07690.10450.2269-0.0215-0.01950.3157-0.03350.2894-16.889135.8867-27.9018
43.9301-0.81972.30682.4233-1.58573.0403-0.25440.29910.198-0.00070.11430.36390.0368-0.23540.14010.1668-0.01180.00960.4758-0.00010.326-49.12433.2815-39.494
511.5391-2.21672.75272.9853-1.2885.91630.01531.15030.1603-0.2332-0.0840.33130.0248-0.27530.06870.2186-0.0642-0.02290.41410.05290.3112-50.632132.691-43.8769
612.6114-3.63065.53094.2959-2.99567.2851-0.3170.10730.04740.10940.36620.5717-0.4291-0.3833-0.04930.1968-0.0209-0.00370.3752-0.02440.3608-51.202134.8651-34.5095
7-9.252-7.16232.09211.0753-4.48570.7948-1.0158-0.8186-0.5578-0.38090.95530.3834-0.349-1.24290.06050.8415-0.0718-0.11071.34280.32721.4533-79.285219.6943-30.4054
87.29070.2714-0.79581.7316-0.58282.09020.0546-0.2165-0.3039-0.12640.05310.36210.2164-0.1684-0.10770.228-0.06340.03240.38720.05480.3539-55.926612.9443-26.8998
94.2068-0.1616-1.91410.8446-0.12981.2559-0.27660.1664-0.48170.08740.08380.1010.265-0.08980.19280.1924-0.03820.0090.4161-0.00320.3301-37.650912.4665-34.1646
109.8785-3.3464-2.92736.53430.830610.7760.0980.39550.4945-0.3050.0478-0.3166-0.55790.1674-0.14580.1773-0.0171-0.01260.2992-0.03270.3236-17.245522.7592-42.0681
118.4859-0.8404-3.5322.72271.17995.4716-0.01790.53050.0251-0.15880.0857-0.3215-0.16090.0829-0.06780.1823-0.0261-0.02610.3296-0.00030.2932-16.919316.3968-43.7921
1212.6383-1.747-7.50682.2504-1.955610.5467-0.6351-0.4562-0.3534-0.14230.0825-0.30311.2330.34170.55260.24410.0214-0.03570.3833-0.03340.4036-16.530413.4725-36.4964
137.1983-2.5955-4.87483.03512.193.9127-0.1815-1.42830.5461-0.07240.3242-0.58860.06890.653-0.14280.1736-0.03950.02350.61160.07760.48715.21735.3109-8.5223
147.9515-0.5517-1.45871.54731.00921.23370.00410.42590.1032-0.3603-0.0587-0.2091-0.0934-0.03980.05450.2178-0.03220.03480.38580.1020.3314-5.37624.3698-18.2849
158.66630.8395-0.52252.02980.1341.3768-0.18490.27670.0061-0.5457-0.0133-0.0661-0.10860.10110.19820.2468-0.03040.03870.44770.04150.2525-5.91934.3066-16.9748
1611.41140.23321.12510.3886-0.23480.72980.08770.4467-0.6592-0.25770.00560.08090.0860.0638-0.09320.2541-0.02990.00330.36610.02410.3241-20.09561.372-13.5126
175.00163.20040.39394.56930.54110.6181-0.159-0.0615-0.26490.00390.1021-0.06710.2143-0.14030.05690.18490.01060.02040.4638-0.03090.312-38.8852-7.5277-6.9887
188.08865.02271.93236.23961.50611.3654-0.0759-0.24320.2084-0.1879-0.10580.5402-0.0779-0.29910.18170.1833-0.00570.00470.4391-0.03640.2471-44.3074-6.8158-8.1465
1916.85662.1054-4.90893.9775-2.21556.4421-0.07681.17670.473-0.08840.25460.73190.2815-1.1298-0.17780.25320.0145-0.02360.6853-0.110.4929-55.47675.98555.1666
205.3-0.5393-1.15222.1134-0.08272.2381-0.0134-0.15660.15330.1838-0.0225-0.0233-0.0525-0.15660.03590.1960.0222-0.0040.3911-0.0750.3318-40.74487.436113.3253
217.49070.1503-0.26450.68850.03190.9885-0.098-0.4196-0.19940.13950.01750.00740.0473-0.03690.08050.19610.01510.01420.4055-0.04550.3214-34.13612.698110.0681
225.6317-2.9181.46212.3592-1.25611.5186-0.1569-0.11780.07960.04050.1022-0.12770.14140.19970.05480.1646-0.01650.04280.42580.05060.3662-6.9778-5.83995.1454
236.5891-3.98060.46056.79830.05282.6716-0.06760.5435-0.3508-0.08920.0336-0.06750.26650.20770.03390.14650.01930.04050.45750.0470.2679-5.5236-10.28194.4087
2410.7337-6.87883.07389.5-3.44384.3683-0.25911.18780.70680.733-0.4692-0.8101-0.44610.91040.72830.1265-0.0438-0.00980.55380.0270.2898-4.7628-0.68276.1112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 10
2X-RAY DIFFRACTION2A11 - 16
3X-RAY DIFFRACTION3A17 - 109
4X-RAY DIFFRACTION4A110 - 148
5X-RAY DIFFRACTION5A149 - 176
6X-RAY DIFFRACTION6A177 - 197
7X-RAY DIFFRACTION7B1 - 8
8X-RAY DIFFRACTION8B9 - 61
9X-RAY DIFFRACTION9B62 - 133
10X-RAY DIFFRACTION10B134 - 153
11X-RAY DIFFRACTION11B154 - 178
12X-RAY DIFFRACTION12B179 - 197
13X-RAY DIFFRACTION13C4 - 16
14X-RAY DIFFRACTION14C17 - 55
15X-RAY DIFFRACTION15C56 - 85
16X-RAY DIFFRACTION16C86 - 110
17X-RAY DIFFRACTION17C111 - 157
18X-RAY DIFFRACTION18C158 - 197
19X-RAY DIFFRACTION19D4 - 14
20X-RAY DIFFRACTION20D15 - 75
21X-RAY DIFFRACTION21D76 - 109
22X-RAY DIFFRACTION22D110 - 148
23X-RAY DIFFRACTION23D149 - 176
24X-RAY DIFFRACTION24D177 - 197

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