[English] 日本語
Yorodumi
- PDB-2kx3: The solution structure of the mutant of UBL domain of UBLCP1, I5M -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kx3
TitleThe solution structure of the mutant of UBL domain of UBLCP1, I5M
ComponentsUbiquitin-like domain-containing CTD phosphatase 1
KeywordsHYDROLASE / UBL domain / UBLCP1 / mutant / CTD-phosphatase
Function / homology
Function and homology information


regulation of proteasome assembly / proteasome regulatory particle binding / negative regulation of ATP-dependent activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / protein dephosphorylation / nucleolus / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIID / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / HAD superfamily / HAD-like superfamily / Ubiquitin-like (UB roll) / Ubiquitin family ...HAD-superfamily hydrolase, subfamily IIID / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / HAD superfamily / HAD-like superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like domain-containing CTD phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLee, N. / Ko, S.
CitationJournal: To be Published
Title: The solution structure of the mutant of UBL domain of UBLCP1, I5M
Authors: Lee, N. / Ko, S.
History
DepositionApr 23, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references
Category: database_2 / 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_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like domain-containing CTD phosphatase 1


Theoretical massNumber of molelcules
Total (without water)9,0161
Polymers9,0161
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

-
Components

#1: Protein Ubiquitin-like domain-containing CTD phosphatase 1


Mass: 9015.708 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-81 / Mutation: I5M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBLCP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q8WVY7, protein-serine/threonine phosphatase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D HBHA(CO)NH
1733D (H)CCH-TOCSY
1813D 1H-15N NOESY
1933D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 15N] UBLI5M-1, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-99% 13C; U-99% 15N] UBLI5M-2, 90% H2O/10% D2O90% H2O/10% D2O
31.5 mM [U-100% 13C] UBLI5M-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMUBLI5M-1[U-99% 15N]1
1.5 mMUBLI5M-2[U-99% 13C; U-99% 15N]2
1.5 mMUBLI5M-3[U-100% 13C]3
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX9002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.5P.GUNTERT ET AL.refinement
CYANA2.2.5P.GUNTERT ET AL.structure solution
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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