[English] 日本語
Yorodumi
- PDB-2roh: The DNA binding domain of RTBP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2roh
TitleThe DNA binding domain of RTBP1
ComponentsTelomere binding protein-1
KeywordsDNA BINDING PROTEIN / telomere binding protein / plant / Nucleus
Function / homology
Function and homology information


regulation of telomere maintenance / telomeric DNA binding / chromosome, telomeric region / protein homodimerization activity
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #220 / Myb-type HTH DNA-binding domain profile. / Serum Albumin; Chain A, Domain 1 / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily ...Serum Albumin; Chain A, Domain 1 - #220 / Myb-type HTH DNA-binding domain profile. / Serum Albumin; Chain A, Domain 1 / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Telomere-binding protein 1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLee, W. / Ko, S.
CitationJournal: Biochemistry / Year: 2009
Title: Solution structure of the DNA binding domain of rice telomere binding protein RTBP1
Authors: Ko, S. / Yu, E.Y. / Shin, J. / Yoo, H.H. / Tanaka, T. / Kim, W.T. / Cho, H.S. / Lee, W. / Chung, I.K.
History
DepositionMar 22, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Telomere binding protein-1


Theoretical massNumber of molelcules
Total (without water)13,8631
Polymers13,8631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein Telomere binding protein-1 / RTBP1


Mass: 13862.783 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9LL45

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1332D 1H-13C HSQC
1433D CBCA(CO)NH
1533D HNCO
1633D HNCA
1733D HN(CA)CB
1833D HBHA(CO)NH
1933D (H)CCH-TOCSY
11033D 1H-15N NOESY
11133D 1H-13C NOESY
11213D HNHA
11323D (H)CCH-TOCSY
11423D 1H-13C NOESY
11513D 1H-15N NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 or 1.3 mM [U-99% 15N] The DNA binding domai of RTBP1, 90% H2O/10% D2O90% H2O/10% D2O
21 or 1.3 mM [U-100% 13C] The DNA binding domai of RTBP1, 100% D2O100% D2O
31 or 1.3 mM [U-99% 13C; U-99% 15N] The DNA binding domai of RTBP1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMThe DNA binding domai of RTBP1[U-99% 15N]1
1 mMThe DNA binding domai of RTBP1[U-100% 13C]2
1 mMThe DNA binding domai of RTBP1[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 150 / pH: 7 / Pressure: AMBIENT / Temperature: 303 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.5Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.2.5Guntert, Mumenthaler and Wuthrichrefinement
CYANABruker Biospin, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAZimmerman, Moseley, Kulikowski and Montelione, Goddardchemical shift assignment
CYANAGoddardpeak picking
CYANACornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / 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