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- PDB-7m5a: Crystal Structure of human BAK in complex with W3W5_BID -

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Basic information

Entry
Database: PDB / ID: 7m5a
TitleCrystal Structure of human BAK in complex with W3W5_BID
Components
  • BH3-interacting domain death agonist p15
  • Bcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / protein-peptide complex
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 / BAK complex / BH domain binding / Activation, myristolyation of BID and translocation to mitochondria / endocrine pancreas development / Release of apoptotic factors from the mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / establishment or maintenance of transmembrane electrochemical gradient ...cysteine-type endopeptidase regulator activity involved in apoptotic process / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / BAK complex / BH domain binding / Activation, myristolyation of BID and translocation to mitochondria / endocrine pancreas development / Release of apoptotic factors from the mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / establishment or maintenance of transmembrane electrochemical gradient / hepatocyte apoptotic process / establishment of protein localization to membrane / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / death receptor binding / regulation of mitochondrial membrane permeability / response to UV-C / apoptotic mitochondrial changes / positive regulation of extrinsic apoptotic signaling pathway / Bcl-2 family protein complex / porin activity / pore complex / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / animal organ regeneration / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to unfolded protein / positive regulation of intrinsic apoptotic signaling pathway / Pyroptosis / Activation of BAD and translocation to mitochondria / neuron apoptotic process / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / signal transduction in response to DNA damage / heat shock protein binding / supramolecular fiber organization / apoptotic signaling pathway / regulation of mitochondrial membrane potential / response to hydrogen peroxide / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of protein-containing complex assembly / cellular response to mechanical stimulus / mitochondrial membrane / cellular response to UV / protein-folding chaperone binding / channel activity / protein-containing complex assembly / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / response to xenobiotic stimulus / apoptotic process / positive regulation of apoptotic process / negative regulation of cell population proliferation / protein heterodimerization activity / negative regulation of gene expression / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSingh, G. / Aggarwal, A. / Moldoveanu, T.
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of BAK activation in mitochondrial apoptosis initiation.
Authors: Singh, G. / Guibao, C.D. / Seetharaman, J. / Aggarwal, A. / Grace, C.R. / McNamara, D.E. / Vaithiyalingam, S. / Waddell, M.B. / Moldoveanu, T.
History
DepositionMar 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)21,3892
Polymers21,3892
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Protein peptide in 1:1 complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-21 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.855, 70.847, 71.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-287-

HOH

21A-321-

HOH

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Components

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


Mass: 18714.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 placI/Y / References: UniProt: Q16611
#2: Protein/peptide BH3-interacting domain death agonist p15 / p15 BID


Mass: 2673.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.43 % / Mosaicity: 0.329 °
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M Potassium Sodium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 26921 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.49 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.019 / Rrim(I) all: 0.052 / Χ2: 1.058 / Net I/σ(I): 13.5 / Num. measured all: 185563
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.90.512620.8570.2350.5560.51796.9
1.53-1.555.50.40613120.9190.1810.4460.58798.7
1.55-1.586.20.38113620.9230.1620.4150.57199.6
1.58-1.626.80.32713060.9490.1340.3540.56699.5
1.62-1.657.10.28113320.9580.1120.3030.51699.3
1.65-1.697.20.23613330.9740.0940.2540.51999.3
1.69-1.737.10.19713520.9810.0790.2120.52399.6
1.73-1.786.80.15913290.9850.0650.1720.57799.4
1.78-1.8360.13313490.9860.0590.1460.60499.4
1.83-1.897.40.11113260.9930.0430.1190.6399.8
1.89-1.967.80.09213390.9960.0350.0990.737100
1.96-2.047.80.07713470.9970.0290.0820.851100
2.04-2.137.50.06413540.9980.0250.0691.06799.8
2.13-2.247.40.05513560.9980.0210.0591.17299.4
2.24-2.387.10.04813400.9990.0190.0521.36499
2.38-2.566.10.04713390.9970.0210.0521.67998.4
2.56-2.827.40.04213660.9990.0170.0461.71999.9
2.82-3.237.80.0413780.9990.0150.0432.02499.9
3.23-4.077.20.03513940.9990.0140.0382.17199.9
4.07-506.50.03314450.9990.0140.0352.14598.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vwz

2vwz


Resolution: 1.5→35.697 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 1257 4.67 %
Rwork0.1851 25660 -
obs0.1866 26917 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.57 Å2 / Biso mean: 22.1179 Å2 / Biso min: 8.64 Å2
Refinement stepCycle: final / Resolution: 1.5→35.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 0 141 1580
Biso mean---33.02 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081480
X-RAY DIFFRACTIONf_angle_d0.942007
X-RAY DIFFRACTIONf_chiral_restr0.076213
X-RAY DIFFRACTIONf_plane_restr0.005262
X-RAY DIFFRACTIONf_dihedral_angle_d2.153805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.55990.25371540.2547272798
1.5599-1.63080.25091430.2154281799
1.6308-1.71680.24461390.1985283099
1.7168-1.82440.28291190.1985284999
1.8244-1.96520.24691610.18882803100
1.9652-2.1630.19961380.17622865100
2.163-2.47590.20241290.1702286299
2.4759-3.11910.18781290.1913290599
3.1191-35.6970.22231450.1774300299

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