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- PDB-2n03: Solution NMR Structure plectin repeat domain 6 (4403-4606) of Ple... -

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Basic information

Entry
Database: PDB / ID: 2n03
TitleSolution NMR Structure plectin repeat domain 6 (4403-4606) of Plectin from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR6354E
ComponentsPlectin
KeywordsSTRUCTURAL PROTEIN / cytoskeletal-linker protein / PSI-BIOLOGY / NESG / Structural Genomics / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / : ...protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / : / regulation of vascular permeability / intermediate filament cytoskeleton organization / dystroglycan binding / cellular response to hydrostatic pressure / fibroblast migration / costamere / T cell chemotaxis / cellular response to fluid shear stress / peripheral nervous system myelin maintenance / cardiac muscle cell development / myoblast differentiation / adherens junction organization / intermediate filament cytoskeleton / response to food / structural constituent of muscle / ankyrin binding / Assembly of collagen fibrils and other multimeric structures / intermediate filament / sarcomere organization / nucleus organization / keratinocyte development / transmission of nerve impulse / brush border / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / establishment of skin barrier / skeletal muscle fiber development / respiratory electron transport chain / mitochondrion organization / wound healing / cell morphogenesis / protein localization / multicellular organism growth / structural constituent of cytoskeleton / sarcolemma / Z disc / cellular response to mechanical stimulus / : / actin filament binding / myelin sheath / gene expression / mitochondrial outer membrane / cadherin binding / axon / focal adhesion / dendrite / perinuclear region of cytoplasm / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
beta-hairpin-alpha-hairpin repeat / Plakin repeat / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat ...beta-hairpin-alpha-hairpin repeat / Plakin repeat / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Plectin/S10, N-terminal / Plectin/S10 domain / Src homology 3 (SH3) domain profile. / SH3 domain / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, distance geometry
Model detailslowest energy, model1
AuthorsPulavarti, S. / Eletsky, A. / Huang, Y. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J. / Montelione, G. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure plectin repeat domain 6 (4403-4606) of Plectin from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR6354E
Authors: Pulavarti, S. / Eletsky, A. / Huang, Y. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J. / Montelione, G. / Szyperski, T.
History
DepositionMar 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plectin


Theoretical massNumber of molelcules
Total (without water)23,7641
Polymers23,7641
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Plectin / / PCN / PLTN / Hemidesmosomal protein 1 / HD1 / Plectin-1


Mass: 23764.014 Da / Num. of mol.: 1 / Fragment: residues 4403-4606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEC, PLEC1 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)magic / References: UniProt: Q15149

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D TROSY-HNCO
1513D TROSY-HNCA
1613D TROSY-HN(CO)CA
1713D TROSY-HN(CA)CB
1813D HMCM[CG]CBCA
1913D HMCMCBCA
11013D [H]-NOESY-[NH/CH] ( mix= 250 ms)
11113D [(H)C]-NOESY-[CH], ( mix = 250 ms)
11223D (H)CCH-COSY, aliphatic
11323D (H)CCH-TOCSY, aliphatic
11423D [H]-NOESY-[NH/CH] ( mix = 70 ms) #
11532D ct [13C,1H] HSQC (ct delay 28 ms)
11632D ct [13C,1H] HSQC (ct delay 42 ms)
11732D ct [13C,1H] HSQC (ct delay 56 ms)

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N; U-2H; ILV-1H] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 mM NaN3, 50 uM DSS, 1 ratio protease inhibitor, 90/10 % H2O/D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 mM NaN3, 50 uM DSS, 1 ratio protease inhibitor, 90/10 % H2O/D2O, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 mM NaN3, 50 uM DSS, 1 ratio protease inhibitor, 90/10 % H2O/D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-100% 13C; U-100% 15N; U-2H; ILV-1H]1
20 mMMES-21
100 mMNaCl-31
5 mMCaCl2-41
10 mMDTT-51
0.02 mMNaN3-61
50 uMDSS-71
1 v/vprotease inhibitor-81
1 mMprotein-10[U-100% 13C; U-100% 15N]2
20 mMMES-112
100 mMNaCl-122
5 mMCaCl2-132
10 mMDTT-142
0.02 mMNaN3-152
50 uMDSS-162
1 v/vprotease inhibitor-172
1 mMprotein-19[U-5% 13C; U-100% 15N]3
20 mMMES-203
100 mMNaCl-213
5 mMCaCl2-223
10 mMDTT-233
0.02 mMNaN3-243
50 uMDSS-253
1 v/vprotease inhibitor-263
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian DDR2VarianDDR26002
Bruker AMXBrukerAMX9003

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Processing

NMR software
NameDeveloperClassification
AutoAssignHuang, Tejero, Powers and Montelionedata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdihedral angles
Rosetta(rosetta) -baker davidrefinement
CARAKeller and Wuthrichdata analysis
PROSAGuntertdata processing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 2914 / NOE intraresidue total count: 373 / NOE long range total count: 880 / NOE medium range total count: 918 / NOE sequential total count: 743 / Protein chi angle constraints total count: 30 / Protein phi angle constraints total count: 111 / Protein psi angle constraints total count: 110
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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