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- PDB-6uxp: Crystal structure of BAK core domain BH3-groove-dimer in complex ... -

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Basic information

Entry
Database: PDB / ID: 6uxp
TitleCrystal structure of BAK core domain BH3-groove-dimer in complex with phosphatidylglycerol
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Pore-forming Protein
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
Chem-PG8 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.492 Å
AuthorsCowan, A.D. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)1059290 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: BAK core dimers bind lipids and can be bridged by them.
Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / ...Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / Smith, B.J. / Reid, G.E. / Dewson, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,35420
Polymers76,0068
Non-polymers4,34912
Water55831
1
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4993
Polymers19,0012
Non-polymers4981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-35 kcal/mol
Surface area8490 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8629
Polymers19,0012
Non-polymers1,8617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-40 kcal/mol
Surface area8660 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9964
Polymers19,0012
Non-polymers9952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-39 kcal/mol
Surface area8970 Å2
MethodPISA
4
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9964
Polymers19,0012
Non-polymers9952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-38 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.161, 51.567, 61.472
Angle α, β, γ (deg.)83.860, 86.130, 87.940
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 9500.688 Da / Num. of mol.: 8 / Fragment: Core/dimerisation domain, residues 68-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q16611
#2: Chemical
ChemComp-PG8 / 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)


Mass: 497.537 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H42O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: magnesium chloride, PEG 4000, tris-chloride

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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: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→37.355 Å / Num. obs: 20718 / % possible obs: 97.1 % / Redundancy: 3.578 % / Biso Wilson estimate: 62.132 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.113 / Χ2: 1.078 / Net I/σ(I): 9.14 / Num. measured all: 74136
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.643.5560.7861.4511705349432920.7310.92494.2
2.64-2.823.6630.5822.2411381320131070.8430.68297.1
2.82-3.053.5870.3853.5710392299828970.9390.45496.6
3.05-3.343.5270.2076.519537276527040.9760.24597.8
3.34-3.733.430.12610.058384249824440.9880.1597.8
3.73-4.33.7370.07816.928213222921980.9940.09198.6
4.3-5.253.6380.06219.916715187218460.9960.07398.6
5.25-7.373.4170.06118.974849145614190.9950.07297.5
7.37-37.3553.650.03729.8929608248110.9980.04498.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.96 Å41.44 Å
Translation2.96 Å41.44 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASER2.8.1phasing
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UXQ

6uxq


Resolution: 2.492→37.355 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2007 9.71 %
Rwork0.1897 18652 -
obs0.1951 20659 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.5 Å2 / Biso mean: 69.9371 Å2 / Biso min: 37.8 Å2
Refinement stepCycle: final / Resolution: 2.492→37.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 153 31 5216
Biso mean--74.84 55.86 -
Num. residues----626
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4923-2.55460.37861300.3502125090
2.5546-2.62360.31691310.2909133097
2.6236-2.70080.34821520.2722133997
2.7008-2.78790.32991410.2557133296
2.7879-2.88760.34351450.2559129996
2.8876-3.00310.27431450.2275133597
3.0031-3.13970.25061480.2119133197
3.1397-3.30520.27771430.1878134097
3.3052-3.51210.21751420.1741134298
3.5121-3.7830.24681530.1746134798
3.783-4.16330.22641460.1573135598
4.1633-4.76470.25611390.1616136999
4.7647-5.9990.20711460.1867133498
5.999-37.3550.20241460.1665134998
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)
12.15411.0729-0.01354.75972.15964.0588-0.044-0.19170.10930.36330.2243-0.255-0.18280.1679-0.18340.40010.0501-0.12280.46060.23350.7285-19.7826-18.9242-24.3531
24.2621-1.36185.08448.10512.09669.5382-0.55610.52110.40670.48460.3214-0.9699-0.95811.44630.12320.4526-0.0965-0.04020.61340.22230.5964-17.3751-18.5827-18.8482
32.1541.44251.02716.77654.76327.77730.0288-0.2872-0.0871-0.3146-0.4166-0.0564-0.6581-0.59950.36980.29290.0311-0.04980.65340.22620.5155-27.05-18.8714-30.9699
43.30966.60450.08688.8599-0.18091.61010.24040.52110.13370.2728-0.0796-0.44240.3052-0.0567-0.15170.29540.0079-0.0420.53390.17290.5642-24.1052-35.3727-31.4778
51.61331.3454-0.57484.8784-0.70193.8241-0.19980.64160.8375-0.35320.46750.6974-0.1226-0.5961-0.22010.4946-0.02350.02590.56760.34180.90134.5659-2.6006-56.4788
62.9015-4.3311-5.4396.35754.38317.61550.22520.4857-0.6082-0.2635-0.17310.8953-0.1513-0.9967-0.14740.3577-0.0624-0.10660.85660.26881.0522-4.129-11.6701-54.9523
79.2852-1.44113.79723.1418-0.49317.86720.44391.20140.3506-0.502-0.4962-0.01120.11310.52150.11980.4492-0.01890.01930.45650.18370.548710.2869-11.2743-62.1624
88.4348-2.55572.16743.41140.81317.1460.0072-0.63920.164-0.0073-0.3119-0.6619-0.00640.70740.16590.3459-0.0664-0.00120.60410.21750.583321.3993-8.7924-44.5564
95.9008-0.75520.13438.001-1.58163.07310.18810.3499-0.4031-0.54370.05090.09830.0320.0206-0.26680.3133-0.0812-0.0720.50820.20240.668514.7586-12.6686-51.3975
103.7478-0.07520.94787.96774.99624.2513-0.0044-0.2067-0.13280.9290.2165-0.59720.91570.0095-0.21460.38480.0112-0.00860.46880.27260.65298.53-25.5859-36.8384
113.09180.2-5.99128.12781.64046.0392-0.26490.3255-0.5203-0.77040.0170.15840.2902-0.28280.25270.35480.0065-0.070.61670.03840.46883.0726-28.8031-51.9413
121.96040.46030.87449.31436.95888.07520.0726-0.1102-0.5664-0.0651-0.2024-0.11690.1261-0.44230.17140.2774-0.0713-0.00240.60290.19120.8598-2.1883-27.0193-36.7225
138.2299-5.88150.09957.65080.05853.90250.0565-0.38790.54120.04420.0831-0.4585-0.2372-0.1217-0.12990.3525-0.0097-0.01760.47440.24340.63220.9386-10.4587-35.8433
146.69983.96834.9237.5117-0.03768.00760.5511-0.3802-0.86130.4417-0.3563-0.61340.6890.3747-0.18540.56070.11320.07060.57220.2620.5894-27.4053-47.2945-11.6615
152.63342.19582.03884.97355.14398.58790.01950.0840.16050.05630.01040.5370.199-0.7455-0.00520.4338-0.04680.00490.59970.34270.6857-38.7811-39.4031-20.0736
164.77315.55480.50278.0924-1.05846.8846-0.09880.34960.95270.5373-0.3450.32550.29090.63740.48010.42490.09450.08020.49880.19340.5956-30.3016-38.8244-5.8037
179.40467.62263.07948.03445.92518.3783-0.20740.3995-0.0221-0.31560.309-2.03630.22821.23-0.04680.58260.18390.00330.87470.34451.2284-11.7685-36.3608-15.1135
185.46071.28021.40152.47984.63734.0562-0.39610.57330.71350.38210.43490.18790.13211.61760.03270.5003-0.0592-0.10920.76590.31140.6499-19.5396-31.507-10.2183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 65 through 124 )G65 - 124
2X-RAY DIFFRACTION2chain 'G' and (resid 125 through 145 )G125 - 145
3X-RAY DIFFRACTION3chain 'H' and (resid 69 through 100 )H69 - 100
4X-RAY DIFFRACTION4chain 'H' and (resid 101 through 148 )H101 - 148
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 106 )A68 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 146 )A107 - 146
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 100 )B71 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 121 )B101 - 121
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 145 )B122 - 145
10X-RAY DIFFRACTION10chain 'C' and (resid 69 through 100 )C69 - 100
11X-RAY DIFFRACTION11chain 'C' and (resid 101 through 144 )C101 - 144
12X-RAY DIFFRACTION12chain 'D' and (resid 69 through 100 )D69 - 100
13X-RAY DIFFRACTION13chain 'D' and (resid 101 through 147 )D101 - 147
14X-RAY DIFFRACTION14chain 'E' and (resid 70 through 100 )E70 - 100
15X-RAY DIFFRACTION15chain 'E' and (resid 101 through 145 )E101 - 145
16X-RAY DIFFRACTION16chain 'F' and (resid 69 through 100 )F69 - 100
17X-RAY DIFFRACTION17chain 'F' and (resid 101 through 124 )F101 - 124
18X-RAY DIFFRACTION18chain 'F' and (resid 125 through 148 )F125 - 148

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