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- PDB-8zug: Human Keratin 19 head domain segment Y6-G28 in solution -

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Basic information

Entry
Database: PDB / ID: 8zug
TitleHuman Keratin 19 head domain segment Y6-G28 in solution
ComponentsKeratin, type I cytoskeletal 19
KeywordsCYTOSOLIC PROTEIN / K19 / IDP
Function / homology
Function and homology information


cell differentiation involved in embryonic placenta development / Keratinization / terminal web / intermediate filament organization / Formation of the cornified envelope / apicolateral plasma membrane / costamere / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / structural constituent of muscle / intermediate filament ...cell differentiation involved in embryonic placenta development / Keratinization / terminal web / intermediate filament organization / Formation of the cornified envelope / apicolateral plasma membrane / costamere / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / structural constituent of muscle / intermediate filament / sarcomere organization / epithelial cell differentiation / Notch signaling pathway / cell periphery / structural constituent of cytoskeleton / sarcolemma / Z disc / response to estrogen / cytoskeleton / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Keratin, type I / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein
Similarity search - Domain/homology
Keratin, type I cytoskeletal 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJi, Y. / Jeong, M. / Kim, J. / Lee, C.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1I1A2074335 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A2C1099696 Korea, Republic Of
CitationJournal: To Be Published
Title: Human Keratin 19 head domain segment Y6-G28 in solution
Authors: Ji, Y. / Jeong, M. / Kim, J. / Lee, C.H.
History
DepositionJun 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Keratin, type I cytoskeletal 19


Theoretical massNumber of molelcules
Total (without water)2,2341
Polymers2,2341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Keratin, type I cytoskeletal 19 / Cytokeratin-19 / CK-19 / Keratin-19 / K19


Mass: 2234.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08727

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-1H NOESY
151isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 3.3 mg/mL Keratin 19 (Y6-G28), 20 mM sodium phosphate, 7 % [U-2H] D2O, 93% H2O/7% D2O
Label: Sample / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.3 mg/mLKeratin 19 (Y6-G28)natural abundance1
20 mMsodium phosphatenatural abundance1
7 %D2O[U-2H]1
Sample conditionsIonic strength: 20 mM / Label: pH / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYWoonghee Leechemical shift assignment
NMRFAM-SPARKYWoonghee Leepeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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