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- PDB-8spf: Crystal structure of Bax core domain BH3-groove dimer - hexameric... -

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Basic information

Entry
Database: PDB / ID: 8spf
TitleCrystal structure of Bax core domain BH3-groove dimer - hexameric fraction with 2-stearoyl lysoPC
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / BAX / BCL2
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / ectopic germ cell programmed cell death / cellular response to unfolded protein / blood vessel remodeling / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / response to gamma radiation / apoptotic signaling pathway / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cerebral cortex development / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process
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
SN-GLYCEROL-1-PHOSPHATE / DODECANE / nonane / N-OCTANE / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCowan, A.D. / Miller, M.S. / Czabotar, P.E. / Colman, P.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Febs J. / Year: 2023
Title: Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids.
Authors: Miller, M.S. / Cowan, A.D. / Brouwer, J.M. / Smyth, S.T. / Peng, L. / Wardak, A.Z. / Uren, R.T. / Luo, C. / Roy, M.J. / Shah, S. / Tan, Z. / Reid, G.E. / Colman, P.M. / Czabotar, P.E.
History
DepositionMay 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX
E: Apoptosis regulator BAX
F: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,72915
Polymers53,8336
Non-polymers8959
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-94 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.134, 83.884, 100.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules CDABEF

#1: Protein
Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 8972.228 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812

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Non-polymers , 6 types, 24 molecules

#2: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#6: Chemical ChemComp-DD9 / nonane / Nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Hepes pH 7.5, 1.4 M trisodium citrate

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 26715 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Net I/σ(I): 15.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.332.01640560.32.2791
2.33-2.491.12639970.6291.2241
2.49-2.690.58537700.8690.6331
2.69-2.950.31734830.9570.3441
2.95-3.290.13531530.9920.1471
3.29-3.80.0628180.9980.0661
3.8-4.650.03823890.9990.0411
4.65-6.530.03219040.9990.0351
6.53-500.022114510.0251

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Processing

Software
NameVersionClassification
PHENIX(dev_3965: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.32 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3055 1992 7.5 %
Rwork0.2526 --
obs0.2566 26576 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 59 15 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013321
X-RAY DIFFRACTIONf_angle_d0.3784450
X-RAY DIFFRACTIONf_dihedral_angle_d11.8951166
X-RAY DIFFRACTIONf_chiral_restr0.03499
X-RAY DIFFRACTIONf_plane_restr0.002564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.45021250.42291506X-RAY DIFFRACTION85
2.25-2.320.32981360.37571685X-RAY DIFFRACTION98
2.32-2.380.39131410.33931739X-RAY DIFFRACTION100
2.38-2.460.34231430.30891771X-RAY DIFFRACTION100
2.46-2.550.3441430.28731756X-RAY DIFFRACTION100
2.55-2.650.30061410.28591759X-RAY DIFFRACTION100
2.65-2.770.31751430.29361750X-RAY DIFFRACTION100
2.77-2.920.3581430.30431768X-RAY DIFFRACTION100
2.92-3.10.3661430.2991770X-RAY DIFFRACTION100
3.1-3.340.32091440.26091766X-RAY DIFFRACTION100
3.34-3.670.28941450.25771788X-RAY DIFFRACTION100
3.67-4.20.28931440.22911794X-RAY DIFFRACTION100
4.21-5.30.28321470.2251819X-RAY DIFFRACTION100
5.3-44.320.29831540.2381913X-RAY DIFFRACTION100
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)
19.35663.66783.86218.25816.91721.99253.6201-5.064710.53951.1084-0.67745.0064-5.70160.2463-4.56281.3656-0.53860.72291.991-0.16252.53176.21817.94632.269
24.0775.3369-3.95927.2155-5.39687.6035-0.479-0.7134-1.1526-0.4088-0.2339-3.69980.01461.44331.01320.7933-0.02770.08350.98880.16830.88435.4224.12124.843
33.1640.91370.07588.3621-2.71127.0177-0.1593-0.26540.3986-0.56350.08880.9029-1.44860.10640.04340.7098-0.0009-0.06160.73070.19770.5949-3.6667.45231.276
42.2289-0.27820.23649.6433-2.78294.03160.653-0.1795-0.69790.5187-0.9673-1.9812-0.571.15040.26680.5264-0.00630.08020.94590.1490.55931.775-4.41834.298
52.69091.00783.59743.11062.11764.0761-0.23950.07590.10610.50080.86260.6425-0.25230.5234-0.36840.48560.06670.10320.81430.04450.7672-22.378-7.37335.112
64.05273.57121.79743.50071.85513.3643-1.8899-1.69870.37811.0977-0.5333-0.6318-1.3669-4.36882.25171.22810.0333-0.10511.0401-0.25691.2953-16.6254.76244.04
74.28250.81582.04386.31721.59324.0412-0.61710.37750.9556-0.94070.23270.29840.32240.57180.31030.68820.05050.04670.70890.0760.5085-13.082-3.87730.69
85.009-4.259-4.26916.73377.00836.33420.06890.15210.7150.07130.402-1.84610.35370.6846-0.34320.66690.0253-0.10280.7995-0.06490.91115.12210.8836.767
93.67270.169-4.34435.4135-1.08035.09080.25070.8531-0.20620.10370.02050.5214-1.3853-1.0236-0.36680.76850.17770.01640.7665-0.00510.7307-15.21624.65610.531
106.71124.74613.15647.60533.28524.9430.2432-0.0260.17710.0211-0.32960.581-0.9309-0.89380.09630.44720.03250.06670.6135-0.04470.4541-14.12115.4649.316
113.1782-4.2289-0.38844.67412.14885.86230.35870.2882-0.2678-1.3383-0.21120.3364-1.0274-0.7449-0.08130.610.0557-0.05680.8103-0.09710.7332-12.43419.6781.382
123.8962-1.75964.92767.8304-4.50177.11740.08620.9923-0.614-0.6413-0.3521-0.02611.75942.07960.52820.80050.2357-0.04760.9263-0.10190.73882.4780.6568.07
137.81520.4003-2.46035.382-0.91839.57440.43950.3895-0.38250.5012-0.0761-0.34661.02670.0824-0.30350.54240.0614-0.12780.40480.04380.3704-1.178.67612.682
144.81094.27744.12896.18225.28994.979-0.9313.51751.9707-2.178-2.26512.50150.03091.19432.90051.5045-0.07160.09681.60740.30641.2862-37.0229.76916.403
154.0003-4.16870.174410.4525-2.18247.0901-0.8114-0.55571.16530.62511.09260.1076-0.8736-0.7136-0.10890.72540.1994-0.0290.8926-0.00630.9714-29.9738.70333.235
164.58773.8294-1.16457.85172.49395.0315-0.9978-0.36140.503-0.10850.35463.53811.7146-0.70021.28251.00330.118-0.11681.25170.22761.1763-38.4815.55332.412
176.7345-2.4199-1.0319.34627.81866.63750.04050.43520.36170.8385-0.5218-0.00940.1819-1.29510.39031.3813-0.26730.02581.50450.30240.7907-28.627.0469.523
186.7312-1.7982-0.27017.1919-4.51756.6662-0.7379-1.3699-0.70161.64731.81913.05331.04190.2967-2.08911.1227-0.35170.0012.0980.270.7684-26.0565.51317.942
197.53983.1365-4.25457.4723-4.64059.10531.2611-1.64630.30711.459-1.01860.082-0.71811.1573-0.2410.6094-0.08170.02430.9442-0.02380.5519-9.56-2.21842.584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 82:87 )E82 - 87
2X-RAY DIFFRACTION2( CHAIN E AND RESID 88:106 )E88 - 106
3X-RAY DIFFRACTION3( CHAIN E AND RESID 107:126 )E107 - 126
4X-RAY DIFFRACTION4( CHAIN F AND RESID 50:81 )F50 - 81
5X-RAY DIFFRACTION5( CHAIN F AND RESID 82:99 )F82 - 99
6X-RAY DIFFRACTION6( CHAIN F AND RESID 100:106 )F100 - 106
7X-RAY DIFFRACTION7( CHAIN F AND RESID 107:126 )F107 - 126
8X-RAY DIFFRACTION8( CHAIN A AND RESID 53:72 )A53 - 72
9X-RAY DIFFRACTION9( CHAIN A AND RESID 73:99 )A73 - 99
10X-RAY DIFFRACTION10( CHAIN A AND RESID 100:124 )A100 - 124
11X-RAY DIFFRACTION11( CHAIN B AND RESID 54:72 )B54 - 72
12X-RAY DIFFRACTION12( CHAIN B AND RESID 73:99 )B73 - 99
13X-RAY DIFFRACTION13( CHAIN B AND RESID 100:124 )B100 - 124
14X-RAY DIFFRACTION14( CHAIN C AND RESID 59:72 )C59 - 72
15X-RAY DIFFRACTION15( CHAIN C AND RESID 73:124 )C73 - 124
16X-RAY DIFFRACTION16( CHAIN D AND RESID 54:73 )D54 - 73
17X-RAY DIFFRACTION17( CHAIN D AND RESID 74:106 )D74 - 106
18X-RAY DIFFRACTION18( CHAIN D AND RESID 107:121 )D107 - 121
19X-RAY DIFFRACTION19( CHAIN E AND RESID 49:81 )E49 - 81

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