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- PDB-7m5b: Crystal Structure of human BAK in complex with M3W5_BID -

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Basic information

Entry
Database: PDB / ID: 7m5b
TitleCrystal Structure of human BAK in complex with M3W5_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 / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / Activation, myristolyation of BID and translocation to mitochondria / negative regulation of endoplasmic reticulum calcium ion concentration / positive regulation of fibroblast apoptotic process ...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 / BH domain binding / B cell negative selection / BAK complex / Activation, myristolyation of BID and translocation to mitochondria / negative regulation of endoplasmic reticulum calcium ion concentration / positive regulation of fibroblast apoptotic process / response to fungus / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / B cell apoptotic process / regulation of epithelial cell proliferation / 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 / regulation of mitochondrial membrane permeability / establishment of protein localization to membrane / death receptor binding / calcium ion transport into cytosol / fibroblast apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / response to UV-C / mitochondrial fusion / Bcl-2 family protein complex / positive regulation of mitochondrial membrane potential / myeloid cell homeostasis / protein targeting to mitochondrion / porin activity / thymocyte apoptotic process / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / pore complex / positive regulation of IRE1-mediated unfolded protein response / mitochondrial ATP synthesis coupled electron transport / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / apoptotic mitochondrial changes / vagina development / regulation of T cell proliferation / B cell homeostasis / positive regulation of calcium ion transport into cytosol / regulation of G1/S transition of mitotic cell cycle / positive regulation of proteolysis / signal transduction in response to DNA damage / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / Activation of BAD and translocation to mitochondria / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / epithelial cell proliferation / response to gamma radiation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / establishment of localization in cell / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / channel activity / protein-containing complex assembly / neuron apoptotic process / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / 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 / metal ion binding / identical protein binding / membrane / 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
COPPER (II) ION / BH3-interacting domain death agonist / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Bcl-2 homologous antagonist/killer
D: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1345
Polymers43,0704
Non-polymers641
Water5,477304
1
A: Bcl-2 homologous antagonist/killer
B: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5993
Polymers21,5352
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-27 kcal/mol
Surface area8780 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)21,5352
Polymers21,5352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-25 kcal/mol
Surface area8580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.190, 83.176, 110.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 22 through 49 or (resid 55...
21(chain C and (resid 22 through 62 or (resid 66...
12(chain B and (resid 81 through 103 or (resid 104...
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 22 through 49 or (resid 55...A22 - 49
121(chain A and (resid 22 through 49 or (resid 55...A55 - 56
131(chain A and (resid 22 through 49 or (resid 55...A21 - 185
141(chain A and (resid 22 through 49 or (resid 55...A21 - 185
151(chain A and (resid 22 through 49 or (resid 55...A21 - 185
161(chain A and (resid 22 through 49 or (resid 55...A120
171(chain A and (resid 22 through 49 or (resid 55...A120
181(chain A and (resid 22 through 49 or (resid 55...A21 - 185
191(chain A and (resid 22 through 49 or (resid 55...A21 - 185
1101(chain A and (resid 22 through 49 or (resid 55...A21 - 185
1111(chain A and (resid 22 through 49 or (resid 55...A21 - 185
211(chain C and (resid 22 through 62 or (resid 66...C22 - 62
221(chain C and (resid 22 through 62 or (resid 66...C66 - 68
231(chain C and (resid 22 through 62 or (resid 66...C21 - 185
241(chain C and (resid 22 through 62 or (resid 66...C21 - 185
251(chain C and (resid 22 through 62 or (resid 66...C21 - 185
261(chain C and (resid 22 through 62 or (resid 66...C21 - 185
112(chain B and (resid 81 through 103 or (resid 104...B0
212chain DD81 - 104

NCS ensembles :
ID
1
2

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Components

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


Mass: 18698.918 Da / Num. of mol.: 2
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: 2836.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.75 Å3/Da / Density % sol: 55.2 % / Mosaicity: 0.299 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 15% PEG 4000 0.2 M NaCl 0.1 MES 6.5

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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: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 39200 / % possible obs: 96.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Rrim(I) all: 0.041 / Χ2: 0.915 / Net I/σ(I): 14.3 / Num. measured all: 222410
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.884.20.86316980.6750.4370.9730.75785.2
1.88-1.924.60.82818510.6960.4040.9270.85392.3
1.92-1.9550.77618800.6980.3650.8620.86694.2
1.95-1.995.40.59319720.8480.2740.6560.83598.4
1.99-2.045.70.47319490.9080.2120.520.83897.2
2.04-2.085.70.37819740.9330.1720.4170.88198.8
2.08-2.145.60.28219490.9460.130.3120.8897.4
2.14-2.195.30.21218710.9640.0990.2360.87892.7
2.19-2.265.90.20319550.9670.090.2231.06797.8
2.26-2.336.20.16119640.9840.0690.1760.93398.4
2.33-2.416.30.1320130.9860.0550.1410.87898.7
2.41-2.516.20.10219960.9910.0440.1110.89699.8
2.51-2.636.10.07820010.9940.0330.0850.91498.8
2.63-2.765.90.05820030.9960.0250.0630.87799
2.76-2.945.70.04420120.9960.0190.0480.90399.1
2.94-3.165.40.03318750.9970.0150.0370.95191.5
3.16-3.486.10.02820310.9980.0120.0311.05998.7
3.48-3.996.20.02320550.9980.010.0251.10799.8
3.99-5.0260.01920900.9990.0080.0210.97599.4
5.02-505.60.01620610.9990.0070.0180.79493

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
HKL-20001.11.1_2575data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vwz

2vwz


Resolution: 1.85→37.078 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1811 5.08 %
Rwork0.1697 33859 -
obs0.1715 35670 88.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.42 Å2 / Biso mean: 24.5196 Å2 / Biso min: 6.29 Å2
Refinement stepCycle: final / Resolution: 1.85→37.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 1 304 3205
Biso mean--17.35 34.15 -
Num. residues----366
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A930X-RAY DIFFRACTION8.656TORSIONAL
12C930X-RAY DIFFRACTION8.656TORSIONAL
21B144X-RAY DIFFRACTION8.656TORSIONAL
22D144X-RAY DIFFRACTION8.656TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.90010.3361650.3069148651
1.9001-1.9560.2665910.2598183963
1.956-2.01910.26411230.2115224278
2.0191-2.09130.23111480.1953259190
2.0913-2.1750.20711430.1727260991
2.175-2.2740.22571460.1718280296
2.274-2.39380.20381670.1639286099
2.3938-2.54380.21341700.1675285899
2.5438-2.74010.21561570.166288799
2.7401-3.01580.21351580.162290899
3.0158-3.45190.20271260.1646281694
3.4519-4.34790.16061630.14612975100
4.3479-37.0780.19581540.1667298695
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.42280.8293-0.09870.8291-0.00521.6147-0.12920.1998-0.1648-0.43010.08030.06770.3777-0.19-0.01530.3038-0.06560.02950.16680.0160.116210.392141.924553.9402
20.9470.59610.69631.11550.32590.754-0.03660.1112-0.1631-0.25230.0726-0.14530.04640.26811.08050.1390.03640.02890.16190.03330.13918.641943.780763.1806
30.4775-0.1163-0.06910.58750.00940.927-0.02070.05430.0467-0.1470.03010.0572-0.0202-0.0478-0.11280.09410.0001-0.00450.09780.06160.07299.967349.170262.4943
41.1911-0.12060.3320.99510.20170.9384-0.0216-0.15030.0735-0.01640.0104-0.1472-0.09850.0233-0.09420.0602-0.0376-0.01240.1450.02850.124220.776753.461966.4133
50.7356-0.60330.33650.79060.29681.2624-0.0151-0.19050.15680.1998-0.01030.03580.09520.1526-0.20460.1833-0.0060.03260.1297-0.06270.116343.635463.159987.0324
63.91630.21820.53231.62770.70580.87460.0451-0.3412-0.11670.4918-0.04920.10560.2561-0.00180.08080.27110.00940.03110.1681-0.07570.139540.108662.425592.2884
70.07640.0347-0.13420.0158-0.0610.2359-0.0693-0.47220.01850.22810.11950.15040.0462-0.14960.01220.1709-0.01430.00120.2639-0.01970.337429.533150.344880.4454
82.04780.5013-0.18281.27861.09411.7119-0.0376-0.0754-0.05960.08320.04130.00630.06940.0844-0.00160.07330.0077-0.00830.0867-0.00870.084743.296356.481778.9301
91.31650.01060.17240.8109-0.26950.6034-0.1401-0.09010.2428-0.05750.0294-0.0262-0.1505-0.1086-0.11380.10120.0064-0.07560.1797-0.01550.229332.323357.355272.8908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 69 )A21 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 106 )A70 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 185 )A107 - 185
4X-RAY DIFFRACTION4chain 'B' and (resid 80 through 104 )B80 - 104
5X-RAY DIFFRACTION5chain 'C' and (resid 21 through 47 )C21 - 47
6X-RAY DIFFRACTION6chain 'C' and (resid 48 through 82 )C48 - 82
7X-RAY DIFFRACTION7chain 'C' and (resid 83 through 100 )C83 - 100
8X-RAY DIFFRACTION8chain 'C' and (resid 101 through 185 )C101 - 185
9X-RAY DIFFRACTION9chain 'D' and (resid 81 through 104 )D81 - 104

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