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- PDB-1f95: SOLUTION STRUCTURE OF DYNEIN LIGHT CHAIN 8 (DLC8) AND BIM PEPTIDE... -

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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 / nitric-oxide synthase inhibitor activity / 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 ...Activation of BIM and translocation to mitochondria / nitric-oxide synthase inhibitor activity / 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 / positive regulation of non-motile cilium assembly / Separation of Sister Chromatids / COPI-mediated anterograde transport / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / Macroautophagy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / intraciliary retrograde transport / RUNX3 regulates BCL2L11 (BIM) transcription / mitocytosis / positive regulation of mitochondrial membrane permeability involved in apoptotic process / motile cilium assembly / MHC class II antigen presentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / 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 / mammary gland development / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / dynein complex / cytoplasmic dynein complex / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / Neutrophil degranulation / myeloid cell homeostasis / dynein intermediate chain binding / NRAGE signals death through JNK / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / thymocyte apoptotic process / FOXO-mediated transcription of cell death genes / spermatid development / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / B cell homeostasis / enzyme inhibitor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / axon cytoplasm / FLT3 Signaling / nitric-oxide synthase regulator activity / endomembrane system / response to endoplasmic reticulum stress / regulation of mitochondrial membrane potential / secretory granule / thymus development / cell-matrix adhesion / post-embryonic development / kidney development / positive regulation of protein-containing complex assembly / kinetochore / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / mitotic spindle / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / site of double-strand break / microtubule binding / scaffold protein binding / regulation of apoptotic process / spermatogenesis / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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NMR measurement

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

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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

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