[English] 日本語
Yorodumi
- PDB-1uvf: Solution Structure of the structured part of the 15th Domain of LEKTI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uvf
TitleSolution Structure of the structured part of the 15th Domain of LEKTI
ComponentsSERINE PROTEINASE INHIBITOR KAZAL TYPE 5
KeywordsSERINE PROTEINASE INHIBITOR / TRYPSIN INHIBITOR / KAZAL / PROTEASE
Function / homology
Function and homology information


negative regulation of antibacterial peptide production / epidermal lamellar body / regulation of timing of anagen / epidermal cell differentiation / hair cell differentiation / Formation of the cornified envelope / negative regulation of immune response / regulation of T cell differentiation / regulation of cell adhesion / epithelial cell differentiation ...negative regulation of antibacterial peptide production / epidermal lamellar body / regulation of timing of anagen / epidermal cell differentiation / hair cell differentiation / Formation of the cornified envelope / negative regulation of immune response / regulation of T cell differentiation / regulation of cell adhesion / epithelial cell differentiation / extracellular matrix organization / negative regulation of angiogenesis / central nervous system development / negative regulation of proteolysis / serine-type endopeptidase inhibitor activity / cell cortex / cell differentiation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular region / cytosol / cytoplasm
Similarity search - Function
Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine protease inhibitor Kazal-type 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVitzithum, K. / Roesch, P. / Marx, U.C.
CitationJournal: Biochemistry / Year: 2004
Title: The Solution Structure of a Chimeric Lekti Domain Reveals a Chameleon Sequence
Authors: Tidow, H. / Lauber, T. / Vitzithum, K. / Sommerhoff, C. / Roesch, P. / Marx, U.C.
History
DepositionJan 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE PROTEINASE INHIBITOR KAZAL TYPE 5


Theoretical massNumber of molelcules
Total (without water)6,9391
Polymers6,9391
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)31 / 200LOWEST ENERGY; LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein SERINE PROTEINASE INHIBITOR KAZAL TYPE 5 / / LYMPHO-EPITHELIAL / KAZAL-TYPE RELATED INHIBITOR / LEKTI


Mass: 6938.950 Da / Num. of mol.: 1 / Fragment: SHORT LEKTI-DOMAIN15, RESIDUES 989-1047
Source method: isolated from a genetically manipulated source
Details: DISULPHIDE BONDS BETWEEN CYS5 AND CYS40, BETWEEN CYS18 AND CYS37 AND BETWEEN CYS26 AND CYS58
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: VAGINAL EPITHELIUM / Plasmid: PET32-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI / Variant (production host): DE3 / References: UniProt: Q9NQ38
Compound detailsFUNCTION: SERINE PROTEASE INHIBITOR, PROBABLY IMPORTANT FOR THE ANTI-INFLAMMATORY AND/OR ...FUNCTION: SERINE PROTEASE INHIBITOR, PROBABLY IMPORTANT FOR THE ANTI-INFLAMMATORY AND/OR ANTIMICROBIAL PROTECTION OF MUCOUS EPITHELIA.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-TOCSY
1212D-COSY
1312D-NOESY
1411H
15115N-HSQC
161HNHA
1713D-1H
1811H
19115N-TOCSY-HSQC
11013D-1H
11111H
112115N-NOESY-HSQC
11313D-1H
114115N
115115N-HMQC-NOESY-HSQC
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD NMR-TECHNIQUES ON 15N-LABELED AND UNLABELED PROTEIN

-
Sample preparation

DetailsContents: 90% H20/10% D2O
Sample conditionsIonic strength: 20 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8.51BRUNGERrefinement
NDEEstructure solution
NMRVIEW5.0.4structure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SIMULATED ANNEALING
NMR ensembleConformer selection criteria: LOWEST ENERGY; LEAST RESTRAINT VIOLATION
Conformers calculated total number: 200 / Conformers submitted total number: 31

+
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