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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 / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / B cell negative selection / BAK complex / response to fungus / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / Activation, myristolyation of BID and translocation to mitochondria ...cysteine-type endopeptidase regulator activity involved in apoptotic process / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / B cell negative selection / BAK complex / response to fungus / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / Activation, myristolyation of BID and translocation to mitochondria / limb morphogenesis / response to mycotoxin / Release of apoptotic factors from the mitochondria / endocrine pancreas development / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / establishment of protein localization to membrane / death receptor binding / calcium ion transport into cytosol / fibroblast apoptotic process / regulation of mitochondrial membrane permeability / mitochondrial fusion / myeloid cell homeostasis / response to UV-C / Bcl-2 family protein complex / positive regulation of extrinsic apoptotic signaling pathway / hepatocyte apoptotic process / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / porin activity / B cell homeostasis / positive regulation of IRE1-mediated unfolded protein response / pore complex / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / vagina development / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of proteolysis / animal organ regeneration / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / positive regulation of calcium ion transport into cytosol / Activation of BAD and translocation to mitochondria / Pyroptosis / blood vessel remodeling / epithelial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / signal transduction in response to DNA damage / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / heat shock protein binding / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / response to gamma radiation / apoptotic signaling pathway / response to hydrogen peroxide / cellular response to mechanical stimulus / positive regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / neuron apoptotic process / protein-folding chaperone binding / channel activity / protein-containing complex assembly / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / 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 / metal ion binding / identical protein binding / cytosol
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / 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
Revision 2.1Oct 9, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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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
Water00
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
Has protein modificationY

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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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