[English] 日本語
Yorodumi
- PDB-2l58: Solution structure of the cytosolic fragment 22-53 of Bcl-2 membe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l58
TitleSolution structure of the cytosolic fragment 22-53 of Bcl-2 member Harakiri
ComponentsActivator of apoptosis harakiri
KeywordsAPOPTOSIS / Bcl-2 / BH3-only / Harakiri / intrinsically disordered protein
Function / homology
Function and homology information


positive regulation of release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / positive regulation of apoptotic process / apoptotic process / mitochondrion / membrane
Similarity search - Function
Activator of apoptosis harakiri / Activator of apoptosis harakiri / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature.
Similarity search - Domain/homology
Activator of apoptosis harakiri
Similarity search - Component
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsBarrera-Vilarmau, S. / Obregon, P. / de Alba, E.
CitationJournal: Plos One / Year: 2011
Title: Intrinsic order and disorder in the bcl-2 member harakiri: insights into its proapoptotic activity.
Authors: Barrera-Vilarmau, S. / Obregon, P. / de Alba, E.
History
DepositionOct 28, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Activator of apoptosis harakiri


Theoretical massNumber of molelcules
Total (without water)3,7261
Polymers3,7261
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Activator of apoptosis harakiri / BH3-interacting domain-containing protein 3 / Neuronal death protein DP5


Mass: 3726.374 Da / Num. of mol.: 1 / Fragment: UNP residues 22-53 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others) / References: UniProt: O00198

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N SOFAST HMQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-13C HSQC
1513D [1H-1H]-TOCSY-[1H-13C]-HSQC
1622D 1H-15N SOFAST HMQC
1722D 1H-1H TOCSY
1822D 1H-1H NOESY
1922D 1H-13C HSQC
11023D [1H-1H]-TOCSY-[1H-13C]-HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0-1.5 mM Hrk-22_53, 0.1 mM sodium azide, 20 mM sodium phosphate, 35% v/v d3 TFE, 100% D2Osample_1100% D2O
solution21.0-1.5 mM Hrk-22_53, 0.1 mM sodium azide, 20 mM sodium phosphate, 35% v/v d2 TFE, 95% H2O/5% D2Osample_295% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMHrk-22_53natural abundance1.0-1.51
0.1 mMsodium azidenatural abundance1
20 mMsodium phosphatenatural abundance1
35 v/vTFEd31
mMHrk-22_53natural abundance1.0-1.52
0.1 mMsodium azidenatural abundance2
20 mMsodium phosphatenatural abundance2
35 v/vTFEd22
Sample conditionsIonic strength: 0.1 / pH: 5.8 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
PIPPGarrettdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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