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- PDB-8ovu: Human titin immunoglobulin-like 21 domain -

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Basic information

Entry
Database: PDB / ID: 8ovu
TitleHuman titin immunoglobulin-like 21 domain
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / Titin / Muscle / Immunoglobulin-like
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 / 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: 1.95 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
DepositionApr 26, 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

Downloads & links

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Assembly

Deposited unit
A: Titin
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5613
Polymers21,5362
Non-polymers241
Water3,405189
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)10,7681
Polymers10,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7932
Polymers10,7681
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.370, 62.163, 189.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

21B-269-

HOH

31B-286-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSER(chain 'A' and (resid 1 through 48))AA1 - 471 - 47
12TYRTYRGLUGLU(chain 'A' and (resid 50 through 99))AA50 - 9850 - 98
21GLYGLYSERSER(chain 'B' and (resid 1 through 48))BB1 - 471 - 47
22TYRTYRGLUGLU(chain 'B' and (resid 50 through 99))BB50 - 9850 - 98

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Components

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


Mass: 10768.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pTEM14 / Details (production host): HisTag cleavable by 3C protease / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8WZ42
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.06 M divalent ions (CaCl2, MgCl2), 0.1 M sodium HEPES, pH 7.5, 50% v/v Polyethylene glycol monomethyl ether (PEGMME) 550, PEG 20K from Morpheus HT-96 screening plate (Molecular Dimensions)

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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: P14 (MX2) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→31.39 Å / Num. obs: 15822 / % possible obs: 97.07 % / Redundancy: 11.3 % / Biso Wilson estimate: 25.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Net I/σ(I): 20.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.473 / Num. unique obs: 1041 / CC1/2: 0.938 / Rpim(I) all: 0.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.18.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→31.39 Å / SU ML: 0.1947 / Cross valid method: FREE R-VALUE / Phase error: 24.3369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 778 4.94 %
Rwork0.1888 14960 -
obs0.1912 15738 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.92 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 1 189 1702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141544
X-RAY DIFFRACTIONf_angle_d1.19252090
X-RAY DIFFRACTIONf_chiral_restr0.0704238
X-RAY DIFFRACTIONf_plane_restr0.0093264
X-RAY DIFFRACTIONf_dihedral_angle_d6.2289204
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection% reflection
Rfree0.2707 93 -
Rwork0.1943 1380 -
obs--91.2 %
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)
10.0758309133418-0.0515969517477-0.1122665275310.04991009530410.06361367916980.170706027686-0.2056186641510.03537815604420.4247951457310.116064925342-0.1181880670270.151771474687-0.263176765712-0.0207114502833-0.0004738822327280.1990128937130.0249539237453-0.0247656420060.23264018307-0.02635579877250.194661979096-11.173735351526.5468029359.82691630914
20.310852532410.217976070058-0.3026461662310.199442583983-0.1467461147240.339720428568-0.271633543494-0.3491638819190.02283025471150.1486544437870.125838077403-0.132003746776-0.0956234042257-0.0745137532618-0.007287493997980.1454664055330.0340300976255-0.01934963333570.1902357591170.01569145624230.2192876066483.0635816834820.093531694618.3623728571
30.179385587809-0.04872921745010.2531791329190.4144202208390.1930269140360.490236083096-0.1087801801810.264577015838-0.313975363168-0.002414833102170.0736313143550.04556279273180.0535464411061-0.05082320336970.0008125826609660.177484575014-0.004910515598980.001431500885580.205592048909-0.01373308652320.242706309154-3.9910623759213.43484874469.1053253225
40.121781861620.0345269932793-0.02252908562490.0578909658053-0.08248057048550.125803546504-0.149920045840.09017772286770.07494216035920.320194603610.039922541419-0.1549661399260.160714299203-0.1783143500710.0005985654942250.164027945320.01346745694880.02264918583840.18155926738-0.01117507609620.244290399501-5.4415180955514.057045370117.7591344608
50.04533699750280.1785114248780.02180029259261.083966097570.2307154893430.0749698418454-0.283735174315-0.513328331524-0.219331547089-0.3406908906740.210551171196-0.2048773531150.2963304397350.08639022388790.01075319293310.179926361450.04632898797030.02119687164140.2840918068930.008974449987550.24079139861511.270982734110.225338519517.1255660195
60.7052216277610.2328706666610.3128835006570.1169993213720.02949677674850.103302575778-0.1546855003820.005142730390150.08959068503360.03912861576410.0158516750359-0.0226736032259-0.1308910798270.0307057221228-0.03524762981770.1137234959050.0158460918253-0.007549167553880.2373156917720.007806615159140.1893953150663.3520375932718.882452166910.0773128483
70.158010038145-0.1155547299410.1520253192660.0955027180042-0.08261779052340.223741479237-0.0019848912297-0.101752071149-0.05555442424960.03928526745860.0255461206472-0.02563677083560.08959592749180.03284952973620.4101482508620.3769244954110.265287416184-0.1972765959290.396623483008-0.06833667674250.20045020403913.13000707647.5262871366843.1409298083
80.2727923178960.0606696243292-0.02844312201530.1210840379550.2179554602980.428029247593-0.2047620562890.1771864843220.1992095237740.03985906420330.102432487258-0.140136065734-0.08336086319060.1163045898290.003561171152890.2034663967040.0351928928275-0.052315544350.166220293537-0.01566602900980.2133304145213.796897830118.395897979832.6631163805
90.667713706538-0.8829759768070.7809735953862.98959043416-0.7010922015590.9721874319850.171936404293-0.135083524222-0.2409199169030.6444429441010.077851849159-0.3605532002020.544614064340.249790512487-0.6642997990160.906666150560.215525831936-0.2967554474130.211034161405-0.01727631259820.31906541866511.8001642863-0.93490396033741.6197833566
101.916246786350.120917099983-0.7711444793752.193324296291.269648493171.105554211940.4233836636130.213684144486-0.1251631346920.325214887664-0.0188957320785-0.145843005990.756190508750.1881152042020.5510864439030.3936529499-0.0127936555581-0.0546546253520.176998038659-0.01217847985650.172930914894-0.5796804121768.5533315587639.764077314
110.2676951376850.001665447540070.200471188941-0.0005981959010530.01141626229710.1891609345690.230934414057-0.00847863459415-0.1579865216290.3452540274780.04758803997070.1513589252660.491510814967-0.0536459430350.02109657759310.327665078447-0.0552708060845-0.01776512988940.209622619314-0.01969100301130.199252699147-8.0981516023310.077454114836.2452955065
120.651071884858-0.1676593970190.07235098532280.2173134819290.1923906864850.264067395467-0.3344311899630.205355390508-0.4595203045310.4804146930180.1995842716010.173998552170.03918948791450.121669775481-0.04473684780090.2518013509180.0713015673176-0.03739374428480.1707826146460.01037663721370.2209249256453.099698544818.269413047630.8156897607
130.65373420414-0.0894565515835-0.1590525068540.1949963482820.2465058693420.280691151007-0.02504776237850.1386417367480.1338573961380.196788149837-0.08261689890470.02874937885810.2899233595860.0968539680291-0.02642528166830.3059923461580.0599020975876-0.0321780671040.129406170415-0.01773958395450.169531940106-0.64803607359415.315180199438.8029813455
140.981060637838-0.498703037272-0.3813175624620.312033202455-0.02056870193580.948366292086-0.340844379759-0.07224284378240.161734481242-0.177495306484-0.1180081813740.3728155432880.175839986297-0.240199234978-0.9557328257030.360540851777-0.1246085456190.1561034078380.0947083928503-0.1384324520940.406903980518-13.696827776932.561453655327.2168880047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 63 )
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 71 )
6X-RAY DIFFRACTION6chain 'A' and (resid 72 through 99 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 8 )
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 28 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 33 )
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 49 )
12X-RAY DIFFRACTION12chain 'B' and (resid 50 through 63 )
13X-RAY DIFFRACTION13chain 'B' and (resid 64 through 94 )
14X-RAY DIFFRACTION14chain 'B' and (resid 95 through 99 )

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