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- PDB-8p35: Mutant human titin immunoglobulin-like 21 domain - C3575S -

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Basic information

Entry
Database: PDB / ID: 8p35
TitleMutant human titin immunoglobulin-like 21 domain - C3575S
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / Titin / Muscle / Immunoglobulin-like
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / protein kinase A signaling / muscle alpha-actinin binding / cardiac myofibril assembly / mitotic chromosome condensation ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / protein kinase A signaling / muscle alpha-actinin binding / cardiac myofibril assembly / mitotic chromosome condensation / cardiac muscle hypertrophy / cardiac muscle tissue morphogenesis / actinin binding / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / 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 / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMartinez-Martin, I. / Crousilles, A. / Mortensen, S.A. / Alegre-Cebollada, J. / Wilmanns, M.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BIO2017-83640-P Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2020-120426GB-I00 Spain
La Caixa FoundationLCF/BQ/DR20/11790009 Spain
CitationJournal: Cell Rep / Year: 2023
Title: Titin domains with reduced core hydrophobicity cause dilated cardiomyopathy.
Authors: Martinez-Martin, I. / Crousilles, A. / Ochoa, J.P. / Velazquez-Carreras, D. / Mortensen, S.A. / Herrero-Galan, E. / Delgado, J. / Dominguez, F. / Garcia-Pavia, P. / de Sancho, D. / Wilmanns, ...Authors: Martinez-Martin, I. / Crousilles, A. / Ochoa, J.P. / Velazquez-Carreras, D. / Mortensen, S.A. / Herrero-Galan, E. / Delgado, J. / Dominguez, F. / Garcia-Pavia, P. / de Sancho, D. / Wilmanns, M. / Alegre-Cebollada, J.
History
DepositionMay 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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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
E: Titin
F: Titin


Theoretical massNumber of molelcules
Total (without water)64,8556
Polymers64,8556
Non-polymers00
Water3,243180
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)10,8091
Polymers10,8091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin


Theoretical massNumber of molelcules
Total (without water)10,8091
Polymers10,8091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Titin


Theoretical massNumber of molelcules
Total (without water)10,8091
Polymers10,8091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Titin


Theoretical massNumber of molelcules
Total (without water)10,8091
Polymers10,8091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Titin


Theoretical massNumber of molelcules
Total (without water)10,8091
Polymers10,8091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Titin


Theoretical massNumber of molelcules
Total (without water)10,8091
Polymers10,8091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.185, 64.892, 288.038
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 10809.206 Da / Num. of mol.: 6 / Mutation: C3575S
Source method: isolated from a genetically manipulated source
Details: The first N-terminal glycine of the sequence corresponds to a linker used for the cloning strategy and it is followed by the sequence of the mutant human Ig 21 domain. In this mutant the ...Details: The first N-terminal glycine of the sequence corresponds to a linker used for the cloning strategy and it is followed by the sequence of the mutant human Ig 21 domain. In this mutant the native cysteine in position 76 is replaced by a serine.
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pETtrx_1a
Details (production host): Expression vector containing a HisTag and a thioredoxin tag, both cleavable by TEV protease
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium salt, pH 7.5, 25 %(w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→48.21 Å / Num. obs: 35855 / % possible obs: 100 % / Redundancy: 24.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Net I/σ(I): 22.6
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 3088 / CC1/2: 0.984 / Rpim(I) all: 0.116 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.17.1_3660phasing
PHENIX1.18.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.21 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 --
Rwork0.22 --
obs-35756 99.92 %
Displacement parametersBiso mean: 42.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4471 0 0 180 4651
LS refinement shellResolution: 2.2→2.27 Å / Rfactor Rfree: 0.346 / Rfactor Rwork: 0.271

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