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- PDB-2m5b: The NMR structure of the BID-BAK complex -

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Basic information

Entry
Database: PDB / ID: 2m5b
TitleThe NMR structure of the BID-BAK complex
Components
  • Bcl-2 homologous antagonist/killer
  • human_BID_BH3_SAHB
KeywordsAPOPTOSIS / BCL-2 family effector BAK / BH3-only protein BID / effector direct activation / NMR solution structure of BID-BAK complex / mitochondrial outer membrane premeabilization
Function / homology
Function and homology information


cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / response to mycotoxin / Activation, myristolyation of BID and translocation to mitochondria / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis ...cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / response to mycotoxin / Activation, myristolyation of BID and translocation to mitochondria / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / positive regulation of fibroblast apoptotic process / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / 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 / protein targeting to mitochondrion / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of epithelial cell proliferation / activation of cysteine-type endopeptidase activity / establishment of protein localization to membrane / endoplasmic reticulum calcium ion homeostasis / death receptor binding / positive regulation of endoplasmic reticulum unfolded protein response / positive regulation of extrinsic apoptotic signaling pathway / regulation of mitochondrial membrane permeability / positive regulation of mitochondrial membrane potential / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / regulation of T cell proliferation / thymocyte apoptotic process / hepatocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / mitochondrial ATP synthesis coupled electron transport / regulation of G1/S transition of mitotic cell cycle / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of proteolysis / vagina development / B cell homeostasis / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Activation of BAD and translocation to mitochondria / cellular response to unfolded protein / blood vessel remodeling / signal transduction in response to DNA damage / animal organ regeneration / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / protein-containing complex assembly / neuron apoptotic process / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / membrane
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / Blc2-like / Apoptosis Regulator Bcl-x / 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. ...BH3-interacting domain death agonist / BH3 interacting domain (BID) / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BH3-interacting domain death agonist / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics
Model detailsfewest violations, model1
AuthorsMoldoveanu, T. / Grace, C.R. / Kriwacki, R.W. / Green, D.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: BID-induced structural changes in BAK promote apoptosis.
Authors: Moldoveanu, T. / Grace, C.R. / Llambi, F. / Nourse, A. / Fitzgerald, P. / Gehring, K. / Kriwacki, R.W. / Green, D.R.
History
DepositionFeb 19, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: 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_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: human_BID_BH3_SAHB


Theoretical massNumber of molelcules
Total (without water)21,4832
Polymers21,4832
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 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 18950.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK, BAK1, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611
#2: Protein/peptide human_BID_BH3_SAHB


Mass: 2532.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) / References: UniProt: P55957*PLUS

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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
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1512D 1H-1H TOCSY
1612D 1H-1H COSY
1713D CBCA(CO)NH
1813D HNCA
1913D HN(CA)CB
11013D HBHA(CBCACO)NH
11113D 1H (H)CCH-TOCSY
11213D 13C-detected HCC-TOCSY
11312D 1H-15N TROSY
11413D 1H-15N NOESY
11513D 1H-15N TOCSY
11613D 1H-13C NOESY
11713D 1H-13C NOESY aliphatic
11813D 1H-13C NOESY aromatic
11912D 13C-1H TROSY
12013D 13C/15N half-filtered 15N-edited NOESY
12113D 13C/15N half-filtered 13C-edited NOESY

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Sample preparation

DetailsContents: ~0.5 mM [U-98% 13C; U-98% 15N] human cBAK, ~0.5 mM human BID BH3 SAHB, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhuman cBAK-1[U-98% 13C; U-98% 15N]1
0.5 mMhuman BID BH3 SAHB-21
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospinstructure solution
TopSpinKeller and Wuthrichprocessing
TopSpinKeller and Wuthrichchemical shift assignment
TopSpinKeller and Wuthrichstructure solution
TopSpinGuntert, Mumenthaler and Wuthrichprocessing
TopSpinGuntert, Mumenthaler and Wuthrichchemical shift assignment
TopSpinGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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