[English] 日本語
Yorodumi
- PDB-1g5v: SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF THE HUMAN SMN PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g5v
TitleSOLUTION STRUCTURE OF THE TUDOR DOMAIN OF THE HUMAN SMN PROTEIN
ComponentsSURVIVAL MOTOR NEURON PROTEIN 1Survival of motor neuron
KeywordsTRANSLATION / mRNA processing
Function / homology
Function and homology information


Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / Z disc / snRNP Assembly ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / Z disc / snRNP Assembly / nervous system development / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain ...SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / mixed torsion, Cartesian angle dynamics simulated annealing protocol
AuthorsSelenko, P. / Sprangers, R. / Stier, G. / Buehler, D. / Fischer, U. / Sattler, M.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: SMN tudor domain structure and its interaction with the Sm proteins.
Authors: Selenko, P. / Sprangers, R. / Stier, G. / Buhler, D. / Fischer, U. / Sattler, M.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SURVIVAL MOTOR NEURON PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)9,7971
Polymers9,7971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average,lowest energy

-
Components

#1: Protein SURVIVAL MOTOR NEURON PROTEIN 1 / Survival of motor neuron


Mass: 9796.644 Da / Num. of mol.: 1 / Fragment: TUDOR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1 / Plasmid: PET9D / Species (production host): Escherichia coli
Gene (production host): EXPRESSED AS FUSION PROTEIN WITH N-TERMINAL HIS6-GST AND TEV CLEAVAGE SITE
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16637

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
3233D 13C-separated NOESY
131HNHA
141IPAP (dipolar couplings)

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM 15N; 20mM phosphate buffer pH 6.3; 30mM NaCl; 5mM DTT90% H2O/10% D2O
21.0 mM 15N,13C; 20mM phosphate buffer pH 6.3; 30mM NaCl; 5mM DTT90% H2O/10% D2O
31.0 mM 15N,13C; 20mM phosphate buffer pH 6.3; 30mM NaCl; 5mM DTT100% D2O
Sample conditionsIonic strength: 20mM Phosphate 30mM NaCl / pH: 6.3 / Pressure: ambient / Temperature: 295 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6brukercollection
NMRPipeDelaglio,F et al. J. Biomol.NMR 6 277-293(1995)processing
XEASYBartels et al. J.Biomol.NMR 5,1-10(1995)data analysis
CNS0.3bruenger et al. Acta Crystallogr.D Biol. Crystallogr. 54, 905-21 (1998)refinement
RefinementMethod: mixed torsion, Cartesian angle dynamics simulated annealing protocol
Software ordinal: 1
Details: 1402 Unambiguous NOE distance restraints 50 Hydrogen bond restraints 44 HN-N dipolar couplings
NMR representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the ...Conformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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