[English] 日本語
Yorodumi
- PDB-1msz: Solution structure of the R3H domain from human Smubp-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1msz
TitleSolution structure of the R3H domain from human Smubp-2
ComponentsDNA-binding protein SMUBP-2
KeywordsDNA BINDING PROTEIN / R3H fold
Function / homology
Function and homology information


double-stranded DNA helicase activity / RNA secondary structure unwinding / ATP-dependent activity, acting on RNA / DNA duplex unwinding / transcription factor binding / ATP-dependent activity, acting on DNA / DNA helicase activity / 5'-3' RNA helicase activity / ribosome binding / single-stranded DNA binding ...double-stranded DNA helicase activity / RNA secondary structure unwinding / ATP-dependent activity, acting on RNA / DNA duplex unwinding / transcription factor binding / ATP-dependent activity, acting on DNA / DNA helicase activity / 5'-3' RNA helicase activity / ribosome binding / single-stranded DNA binding / 5'-3' DNA helicase activity / growth cone / DNA helicase / tRNA binding / single-stranded RNA binding / nuclear body / RNA helicase / ribonucleoprotein complex / axon / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Helicase SMUBP-2/Hcs1-like / DNA-binding protein SMUBP-2, R3H domain / : / Helicase SMUBP-2/HCS1, 1B domain / R3H-like domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. ...Helicase SMUBP-2/Hcs1-like / DNA-binding protein SMUBP-2, R3H domain / : / Helicase SMUBP-2/HCS1, 1B domain / R3H-like domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / : / DNA2/NAM7 helicase, helicase domain / AAA domain / Ribosomal Protein S8; Chain: A, domain 1 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein SMUBP-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLiepinsh, E. / Leonchiks, A. / Sharipo, A. / Guignard, L. / Otting, G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution structure of the R3H domain from human Smubp-2
Authors: Liepinsh, E. / Leonchiks, A. / Sharipo, A. / Guignard, L. / Otting, G.
History
DepositionSep 20, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding protein SMUBP-2


Theoretical massNumber of molelcules
Total (without water)9,7071
Polymers9,7071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein DNA-binding protein SMUBP-2


Mass: 9706.846 Da / Num. of mol.: 1 / Fragment: R3H domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Smubp-2 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P38935

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: Distance restraints collected from a NOESY spectrum with 40 ms mixing time.

-
Sample preparation

DetailsContents: 0.4mM R3H domain / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: no buffer added / pH: 6.9 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
OPAL2.6Luginbuehlrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: structure based on 663 non-redundant NOEs, 123 coupling constants, and 170 dihedral-angle restraints derived from coupling constants, NOE data and preliminary structure calculations. The ...Details: structure based on 663 non-redundant NOEs, 123 coupling constants, and 170 dihedral-angle restraints derived from coupling constants, NOE data and preliminary structure calculations. The number of Missing residues was so much that remark 465 for the missing residues list were removed.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / 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://pdbjlvh1.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