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- PDB-7k02: The crystal structure of a BAK dimer activated by detergent -

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Basic information

Entry
Database: PDB / ID: 7k02
TitleThe crystal structure of a BAK dimer activated by detergent
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / BAK / BH3-in-groove dimer / BCL-2 fold / pore forming / proapoptotic
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 / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis ...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 / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis / 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 / B 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 / regulation of mitochondrial membrane permeability / 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 / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / negative regulation of peptidyl-serine phosphorylation / 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 / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to gamma radiation / 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 / 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 / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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, 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
Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBirkinshaw, R.W. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1059331 Australia
National Health and Medical Research Council (NHMRC, Australia)1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Mol.Cell / Year: 2021
Title: Structure of detergent-activated BAK dimers derived from the inert monomer.
Authors: Birkinshaw, R.W. / Iyer, S. / Lio, D. / Luo, C.S. / Brouwer, J.M. / Miller, M.S. / Robin, A.Y. / Uren, R.T. / Dewson, G. / Kluck, R.M. / Colman, P.M. / Czabotar, P.E.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Bcl-2 homologous antagonist/killer
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)81,6026
Polymers81,6026
Non-polymers00
Water0
1
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)27,2012
Polymers27,2012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-35 kcal/mol
Surface area14890 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)27,2012
Polymers27,2012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-38 kcal/mol
Surface area14740 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)27,2012
Polymers27,2012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-34 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.320, 115.610, 44.530
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13600.395 Da / Num. of mol.: 6 / Mutation: C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16611

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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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 50% (v/v) methane pentane diol (MPD) and 0.1 M imidazole pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.4→39.33 Å / Num. obs: 11007 / % possible obs: 99.57 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rrim(I) all: 0.05711 / Net I/σ(I): 13.43
Reflection shellResolution: 3.4→3.522 Å / Mean I/σ(I) obs: 1.32 / Num. unique obs: 1083 / CC1/2: 0.484 / Rrim(I) all: 1.222

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UXM

6uxm


Resolution: 3.4→39.33 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3427 555 5.05 %
Rwork0.2961 10430 -
obs0.2983 10985 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 383.08 Å2 / Biso mean: 202.5982 Å2 / Biso min: 81.42 Å2
Refinement stepCycle: final / Resolution: 3.4→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5225 0 0 0 5225
Num. residues----651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.740.36581520.370825922744100
3.74-4.280.35621200.336426082728100
4.28-5.390.36831350.307626142749100
5.39-39.330.3261480.27122616276499
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)
11.81692.00752.30795.14624.67968.1287-0.76470.4292-0.3798-0.8873-0.5631.1261-0.3862-1.46270.77261.5203-0.33620.06842.0618-0.48771.496612.5393-33.51968.5613
22.53891.19370.80648.10242.40631.74120.61790.0139-0.38221.0242-0.94270.19150.3577-0.38730.23731.4912-0.12460.15420.982-0.25220.536425.3835-3.384327.597
31.80630.4528-0.8646.30142.21451.31560.41290.0580.4406-1.3144-0.3365-0.1719-0.2723-0.2227-0.07181.47570.067-0.12710.975-0.16470.571225.5482.982116.9523
43.7582-4.8297-6.03326.55546.620710.119-0.8752-0.53090.18490.6358-0.03770.91310.3074-0.36790.56061.18490.462-0.2121.7459-0.25311.431512.662232.489435.1596
50.93760.5579-0.26074.69521.3075-0.2619-0.8844-0.42561.24252.14843.1069-0.00160.7583-1.14061.61392.41250.7283-0.71623.0658-1.7142.978923.292338.861144.4872
62.5541-0.45470.04734.9722-0.59126.14470.48312.2549-1.9164-2.7102-0.1625-1.9817-1.1851-1.05920.91071.5809-1.35470.61183.1034-1.85022.882624.05372.852343.9984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 69 through 173)A69 - 173
2X-RAY DIFFRACTION2(chain 'B' and resid 67 through 183)B67 - 183
3X-RAY DIFFRACTION3(chain 'C' and resid 67 through 183)C67 - 183
4X-RAY DIFFRACTION4(chain 'D' and resid 68 through 171)D68 - 171
5X-RAY DIFFRACTION5(chain 'E' and resid 69 through 174)E69 - 174
6X-RAY DIFFRACTION6(chain 'F' and resid 67 through 168)F67 - 168

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