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- PDB-6sdb: Chimeric titin Z1Z2 functionalized with a KLER exogenous peptide ... -

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Basic information

Entry
Database: PDB / ID: 6sdb
TitleChimeric titin Z1Z2 functionalized with a KLER exogenous peptide from decorin
ComponentsTitin,Decorin,Titin
KeywordsSTRUCTURAL PROTEIN / titin z1z2
Function / homology
Function and homology information


: / dermatan sulfate biosynthetic process / collagen type VI trimer / Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / extracellular matrix structural constituent conferring compression resistance / chondroitin sulfate catabolic process ...: / dermatan sulfate biosynthetic process / collagen type VI trimer / Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / extracellular matrix structural constituent conferring compression resistance / chondroitin sulfate catabolic process / chondroitin sulfate biosynthetic process / Defective B3GALT6 causes EDSP2 and SEMDJL1 / CS/DS degradation / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / : / A tetrasaccharide linker sequence is required for GAG synthesis / sarcomerogenesis / structural molecule activity conferring elasticity / negative regulation of vascular endothelial growth factor signaling pathway / : / 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 / glycosaminoglycan binding / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / actinin binding / M band / extracellular matrix binding / I band / cardiac muscle cell development / regulation of protein kinase activity / negative regulation of endothelial cell migration / structural constituent of muscle / positive regulation of mitochondrial depolarization / sarcomere organization / positive regulation of mitochondrial fission / skeletal muscle thin filament assembly / striated muscle thin filament / positive regulation of macroautophagy / ECM proteoglycans / positive regulation of autophagy / striated muscle contraction / response to mechanical stimulus / skeletal muscle tissue development / cardiac muscle contraction / protein kinase A signaling / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / lysosomal lumen / negative regulation of angiogenesis / condensed nuclear chromosome / kidney development / muscle contraction / positive regulation of protein secretion / placenta development / animal organ morphogenesis / wound healing / Z disc / Golgi lumen / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / collagen-containing extracellular matrix / protease binding / response to lipopolysaccharide / 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 / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
Decorin / Small leucine-rich proteoglycan, class I, decorin/asporin/byglycan / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain ...Decorin / Small leucine-rich proteoglycan, class I, decorin/asporin/byglycan / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Leucine-rich repeat domain superfamily / 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
ACETATE ION / PHOSPHATE ION / Decorin / Titin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFleming, J.R. / Hill, C. / Mayans, O.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204401/z/16/z United Kingdom
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Int J Mol Sci / Year: 2019
Title: The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications.
Authors: Nesterenko, Y. / Hill, C.J. / Fleming, J.R. / Murray, P. / Mayans, O.
History
DepositionJul 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Titin,Decorin,Titin
B: Titin,Decorin,Titin
C: Titin,Decorin,Titin
D: Titin,Decorin,Titin
E: Titin,Decorin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18519
Polymers105,2835
Non-polymers90314
Water3,639202
1
A: Titin,Decorin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4117
Polymers21,0571
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin,Decorin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2744
Polymers21,0571
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Titin,Decorin,Titin


Theoretical massNumber of molelcules
Total (without water)21,0571
Polymers21,0571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Titin,Decorin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1162
Polymers21,0571
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Titin,Decorin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3295
Polymers21,0571
Non-polymers2724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.200, 149.200, 149.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111(chain 'A' and resid 3 through 97)AA3 - 965 - 98
221(chain 'B' and resid 3 through 97)BB3 - 965 - 98
331(chain 'C' and resid 3 through 97)CC3 - 965 - 98
441(chain 'E' and resid 3 through 97)EE3 - 965 - 98
152(chain 'A' and resid 100 through 193)AA100 - 192102 - 194
262(chain 'B' and resid 100 through 193)BB100 - 192102 - 194
372(chain 'D' and resid 100 through 193)DD100 - 192102 - 194
482(chain 'E' and (resid 100 through 192 or (resid 193...EE100 - 192102 - 194

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Titin,Decorin,Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14 / Bone proteoglycan II / PG-S2 / PG40 / Connectin ...Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14 / Bone proteoglycan II / PG-S2 / PG40 / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 21056.512 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN, DCN, SLRR1B / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZ42, UniProt: P07585, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 216 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.77 Å3/Da / Density % sol: 78.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1 M NH4H2PO4 pH 4.6, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→48.84 Å / Num. obs: 487636 / % possible obs: 93.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 63.56 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.2779 / Rrim(I) all: 0.2799 / Net I/σ(I): 9.62
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 2.541 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 4643 / CC1/2: 0.763 / Rrim(I) all: 2.668 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A38

2a38


Resolution: 2.8→48.84 Å / SU ML: 0.442 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 25.3778
RfactorNum. reflection% reflection
Rfree0.2335 --
Rwork0.1914 --
obs-46607 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 58 202 6142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00966029
X-RAY DIFFRACTIONf_angle_d1.248193
X-RAY DIFFRACTIONf_chiral_restr0.0647960
X-RAY DIFFRACTIONf_plane_restr0.00821081
X-RAY DIFFRACTIONf_dihedral_angle_d11.06633624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.880.39251480.33663519X-RAY DIFFRACTION99.97
2.88-2.920.36411420.33323553X-RAY DIFFRACTION99.92
2.92-2.970.35441420.32793532X-RAY DIFFRACTION99.86
2.97-3.020.37721380.31863568X-RAY DIFFRACTION99.89
3.02-3.070.35621320.30733516X-RAY DIFFRACTION99.95
3.07-3.120.33461350.27293530X-RAY DIFFRACTION99.86
3.12-3.180.2761360.27653543X-RAY DIFFRACTION100
3.18-3.250.31091460.25393539X-RAY DIFFRACTION99.97
3.25-3.320.24371460.23343520X-RAY DIFFRACTION99.97
3.32-3.40.26571400.22123514X-RAY DIFFRACTION99.92
3.4-3.480.29741440.20063543X-RAY DIFFRACTION100
3.48-3.580.25591420.19253529X-RAY DIFFRACTION99.97
3.58-3.680.25951340.18153505X-RAY DIFFRACTION100
3.68-3.80.25321360.1733568X-RAY DIFFRACTION100
3.8-3.940.20121420.17613564X-RAY DIFFRACTION99.97
3.94-4.090.20211380.14163527X-RAY DIFFRACTION100
4.09-4.280.1931500.14213517X-RAY DIFFRACTION99.97
4.28-4.50.18241500.12313543X-RAY DIFFRACTION100
4.5-4.790.17251340.12143525X-RAY DIFFRACTION100
4.79-5.160.16981400.12863557X-RAY DIFFRACTION99.97
5.16-5.670.18581400.1483492X-RAY DIFFRACTION100
5.67-6.490.2191520.17493571X-RAY DIFFRACTION100
6.49-8.180.23351270.1933515X-RAY DIFFRACTION100
8.18-48.840.20511490.2053516X-RAY DIFFRACTION99.3
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)
14.994016470190.413000677678-1.194376423210.905307921123-0.7579830681721.445773024460.0225598619551-0.3669308333990.2804951616890.3027711528140.0594459577777-0.111515629312-0.06959395753980.119081037074-0.09666996680320.5938189159430.0990975006484-0.008518836719360.454908907162-0.08527388555040.39107804563196.4263613588-25.94832595416.56377926052
22.5157778209-0.370128230425-1.668911116594.536355519061.818168778486.749885475870.132047339851-0.1956233935490.2476077457720.141831196097-0.00604566008069-0.310325488899-0.1536557680490.4139523261-0.1042804776710.373054915397-0.0963543185893-0.00124180208430.3865085730210.03761789585530.3887619868771.3928340644-30.010694307341.1179332778
30.304881265512-0.011354570361-0.6910750894681.141258433351.021971505881.739261545720.06092219840120.189805356304-0.0735742636095-0.08201988624590.0601836666073-0.1077580014310.1021111829270.14595585303-0.1339900107350.486651355037-0.0358711755982-0.05785942300150.467525739662-0.04407593127010.42625679476385.607546298110.395652385621.8744874276
45.655968436681.077952778222.069724592084.720862527020.6658381530962.64767517684-0.0168444770190.1685228534180.462457322639-0.423197305269-0.05832746204520.435340298604-0.237948423933-0.1367695613240.155666567750.6522851653940.125339818670.02474751064440.420767208686-0.03088486029760.50155377911880.6028954178-9.135232664641.43531224413
53.97253295835-0.325696515486-3.987397722863.357614487410.3125513670596.65449308835-0.10693744899-0.2536395410760.01820025897170.2537971540930.153418764396-0.3821901808440.0519077490980.384020308759-0.09417882341750.4518540346630.097381880004-0.09038342603110.453939751873-0.1034850776140.491355710598114.959843478-36.1997230401-1.66402212562
63.19389182218-1.13035513461-0.2645085264766.699994542241.508617301444.70276493016-0.16050281378-0.213102110191-0.3208922568030.4933185050850.520397260839-0.8676137906760.2293322386630.771756279814-0.3565743665350.4564060457080.173645489525-0.08014395869440.537782960247-0.1043119082340.687862160167123.244752989-56.3591451809-7.45113278111
74.43401843013-0.245633200407-2.03943493373.166184719841.814521659356.90963458595-0.04150449180850.6311653121520.0652805973872-0.2301961438330.00310513965462-0.203880970151-0.1889150402230.275496469230.04600112749380.329294260837-0.0120816623147-0.04076221767730.6016692730610.05836421940620.41094612272486.4026577909-51.6363408895-64.3144834566
86.423229902821.430144217193.890766299813.332264201611.965128311315.71560557435-0.2677184272050.1759366961090.502376884294-0.3199078979460.15675399417-0.19952777983-0.5469367200790.03833949787670.07758795820190.5479188898910.06924069704060.05986779202440.3686558112532.84027044186E-50.429815094502100.550285469-27.1865550822-23.1850721426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 193)
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 111 )
4X-RAY DIFFRACTION4chain 'B' and (resid 112 through 193)
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 97 )
6X-RAY DIFFRACTION6chain 'D' and (resid 100 through 193 )
7X-RAY DIFFRACTION7chain 'E' and (resid 3 through 97 )
8X-RAY DIFFRACTION8chain 'E' and (resid 98 through 193)

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