[English] 日本語
Yorodumi
- PDB-8xto: Human Keratin 19 head domain segment L18-G38 in solution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xto
TitleHuman Keratin 19 head domain segment L18-G38 in solution
ComponentsKeratin, type I cytoskeletal 19
KeywordsCYTOSOLIC PROTEIN / K19 / Head Domain / 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 / intermediate filament / structural constituent of muscle ...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 / intermediate filament / structural constituent of muscle / sarcomere organization / Notch signaling pathway / epithelial cell differentiation / cell periphery / sarcolemma / structural constituent of cytoskeleton / 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
AuthorsJeong, M. / Ji, Y. / 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 L18-G38 in solution
Authors: Jeong, M. / Ji, Y. / Kim, J. / Lee, C.H.
History
DepositionJan 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Keratin, type I cytoskeletal 19


Theoretical massNumber of molelcules
Total (without water)2,0421
Polymers2,0421
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

-
Components

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


Mass: 2042.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08727
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY

-
Sample preparation

DetailsType: solution
Contents: 3.3 mg/mL Keratin 19 (L18-G38), 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 (L18-G38)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

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leechemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CYANA3.98.15 (macarm-gfortran)Guntert, Mumenthaler and Wuthrichrefinement
TopSpin4.1.4Bruker Biospinprocessing
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
TopSpinBruker Biospincollection
Refinement
MethodSoftware ordinal
simulated annealing2
simulated annealing3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more