[English] 日本語
Yorodumi
- PDB-1f95: SOLUTION STRUCTURE OF DYNEIN LIGHT CHAIN 8 (DLC8) AND BIM PEPTIDE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f95
TitleSOLUTION STRUCTURE OF DYNEIN LIGHT CHAIN 8 (DLC8) AND BIM PEPTIDE COMPLEX
Components
  • BCL2-LIKE 11 (APOPTOSIS FACILITATOR)
  • DYNEIN
KeywordsCONTRACTILE PROTEIN/peptide / dynein / light chain / DLC8 / Bim / APOPTOSIS / CONTRACTILE PROTEIN-peptide complex
Function / homology
Function and homology information


Activation of BIM and translocation to mitochondria / Intraflagellar transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Aggrephagy / Loss of Nlp from mitotic centrosomes ...Activation of BIM and translocation to mitochondria / Intraflagellar transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Aggrephagy / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / Separation of Sister Chromatids / positive regulation of non-motile cilium assembly / nitric-oxide synthase inhibitor activity / Macroautophagy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / BIM-BCL-xl complex / BIM-BCL-2 complex / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / regulation of developmental pigmentation / COPI-mediated anterograde transport / intraciliary retrograde transport / RUNX3 regulates BCL2L11 (BIM) transcription / mitocytosis / positive regulation of mitochondrial membrane permeability involved in apoptotic process / MHC class II antigen presentation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / motile cilium assembly / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / negative regulation of nitric oxide biosynthetic process / COP9 signalosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / mammary gland development / dynein complex / Bcl-2 family protein complex / myeloid cell homeostasis / cytoplasmic dynein complex / Neutrophil degranulation / cellular response to glucocorticoid stimulus / NRAGE signals death through JNK / thymocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / dynein intermediate chain binding / T cell homeostasis / B cell homeostasis / spermatid development / enzyme inhibitor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 Signaling / axon cytoplasm / endomembrane system / response to endoplasmic reticulum stress / secretory granule / thymus development / cell-matrix adhesion / nitric-oxide synthase regulator activity / post-embryonic development / regulation of mitochondrial membrane potential / kidney development / positive regulation of protein-containing complex assembly / kinetochore / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / mitotic spindle / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / site of double-strand break / scaffold protein binding / spermatogenesis / regulation of apoptotic process / microtubule binding / in utero embryonic development / microtubule / mitochondrial outer membrane / cytoskeleton / cilium / positive regulation of apoptotic process / protein domain specific binding
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. ...Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bcl-2-like protein 11 / Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFan, J.-S. / Zhang, Q. / Tochio, H. / Li, M. / Zhang, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain.
Authors: Fan, J. / Zhang, Q. / Tochio, H. / Li, M. / Zhang, M.
History
DepositionJul 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DYNEIN
B: DYNEIN
C: BCL2-LIKE 11 (APOPTOSIS FACILITATOR)
D: BCL2-LIKE 11 (APOPTOSIS FACILITATOR)


Theoretical massNumber of molelcules
Total (without water)22,7664
Polymers22,7664
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)1 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein DYNEIN / PROTEIN INHIBITOR OF NEURONAL NITRIC OXIDE SYNTHASE / DLC8


Mass: 10381.899 Da / Num. of mol.: 2 / Fragment: 8KDA LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / References: UniProt: P63170
#2: Protein/peptide BCL2-LIKE 11 (APOPTOSIS FACILITATOR)


Mass: 1001.114 Da / Num. of mol.: 2 / Fragment: DLC8 BINDING REGION / Source method: obtained synthetically
Details: This peptide was chemically synthesized. This sequence occurs naturally in humans (Homo sapiens)
References: UniProt: O43521

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1332D NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM DLC8/Bim peptide complex 15N; 100mM phosphate buffer; 10mM DTT; 90% H2O and 10% D2O90% H2O and 10% D2O
21.5mM DLC8/Bim peptide complex 15N,13C; 100mM phosphate buffer; 10mM DTT; 90% H2O and 10% D2O90% H2O and 10% D2O
31.5mM DLC8/Bim peptide complex ; 100mM phosphate buffer; 10mM DTT; 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 100mM / pH: 7 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bvariancollection
NMRPipe1.7processing
X-PLOR3.8structure solution
CNS1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 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