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- PDB-2lp8: SOLUTION STRUCTURE OF AN APOPTOSIS ACTIVATING PHOTOSWITCHABLE BAK... -

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Basic information

Entry
Database: PDB / ID: 2lp8
TitleSOLUTION STRUCTURE OF AN APOPTOSIS ACTIVATING PHOTOSWITCHABLE BAK PEPTIDE BOUND to BCL-XL
Components
  • Bcl-2 homologous antagonist/killer
  • Bcl-2-like protein 1
KeywordsAPOPTOSIS/APOPTOSIS ACTIVATOR / APOPTOSIS / AZOBENZENE / PHOTOSWITCH / PHOTOCONTROL / APOPTOSIS INHIBITOR / APOPTOSIS-APOPTOSIS ACTIVATOR complex
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process in bone marrow cell / post-embryonic camera-type eye morphogenesis / SARS-CoV-1-mediated effects on programmed cell death / endocrine pancreas development / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mononuclear cell proliferation / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / positive regulation of calcium ion transport into cytosol / response to cycloheximide / porin activity / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / pore complex / thymocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / ectopic germ cell programmed cell death / blood vessel remodeling / Pyroptosis / animal organ regeneration / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to gamma radiation / synaptic vesicle membrane / cellular response to mechanical stimulus / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-33B / Bcl-2-like protein 1 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWysoczanski, P. / Mart, R.J. / Loveridge, J.E. / Williams, C. / Whittaker, S.B.-M. / Crump, M.P. / Allemann, R.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: NMR Solution Structure of a Photoswitchable Apoptosis Activating Bak Peptide Bound to Bcl-x(L).
Authors: Wysoczanski, P. / Mart, R.J. / Loveridge, E.J. / Williams, C. / Whittaker, S.B. / Crump, M.P. / Allemann, R.K.
History
DepositionFeb 3, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2May 23, 2012Group: Database references
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_spectrometer.model / _struct.pdbx_model_details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 1
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6303
Polymers23,1042
Non-polymers5251
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 21455.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L, BCL2L1, BCLX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 1648.934 Da / Num. of mol.: 1 / Fragment: BH3 domain residues 72-87 / Mutation: Q73C, Q77A, I80A, I81F, D84C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16611
#3: Chemical ChemComp-33B / 3,3'-(E)-diazene-1,2-diylbis{6-[(chloroacetyl)amino]benzenesulfonic acid}


Mass: 525.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14Cl2N4O8S2
Sequence detailsTHE AUTHOR STATES THAT THERE IS A DELETION OF RESIDUES 45-84 AND RESIDUES 210-233. RESIDUES ARE ...THE AUTHOR STATES THAT THERE IS A DELETION OF RESIDUES 45-84 AND RESIDUES 210-233. RESIDUES ARE CONTINUOUSLY NUMBERED IGNORING THE DELETION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D (H)CCH-TOCSY
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D H(CCO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
112213C, 15N F1, F2 FILTERED 2D 1H-1H NOESY
113313C, 15N F1, F2 FILTERED 2D 1H-1H NOESY
114213C, 15N F1, F2 FILTERED 2D 1H-1H TOCSY
115313C, 15N F1, F2 FILTERED 2D 1H-1H TOCSY
116213C, 15N F2f 2D 1H-1H NOESY
117215N F1, F2 FILTERED 2D 1H-1H TOCSY
11813D 1H-15N TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 MM [U-98% 13C U-98% 15N] BCL- XL, 1.1 MM PHOTOSWITCHABLE BAK, 5 MM SODIUM PHOSPHATE, 5 MM 2- MERCAPTOETHANOL, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21 MM [U-98% 13C U-98% 15N] BCL- XL, 1.1 MM PHOTOSWITCHABLE BAK, 5 MM SODIUM PHOSPHATE, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution31 MM [U-98% 13C U-98% 15N] BCL-XL, 1.1 MM PHOTOSWITCHABLE BAK, 5 MM SODIUM PHOSPHATE, 100% D2Osample_390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBCL-XL[U-98% 13C; U-98% 15N]1
1.1 mMPHOTOSWITCHABLE BAKnatural abundance1
5 mMSODIUM PHOSPHATEnatural abundance1
5 mM2-MERCAPTOETHANOLnatural abundance1
1 mMBCL-XL[U-98% 13C; U-98% 15N]2
1.1 mMPHOTOSWITCHABLE BAKnatural abundance2
5 mMSODIUM PHOSPHATEnatural abundance2
1 mMBCL-XL[U-98% 13C; U-98% 15N]3
1.1 mMPHOTOSWITCHABLE BAKnatural abundance3
5 mMSODIUM PHOSPHATEnatural abundance3
Sample conditionsIonic strength: 50 / pH: 7.3 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3638 / NOE intraresidue total count: 1289 / NOE long range total count: 442 / NOE medium range total count: 658 / NOE sequential total count: 753 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 154 / Protein psi angle constraints total count: 154
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 21

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