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- PDB-8svk: Crystal structure of Bax D71N core domain BH3-groove dimer -

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Basic information

Entry
Database: PDB / ID: 8svk
TitleCrystal structure of Bax D71N core domain BH3-groove dimer
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 / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / B cell negative selection / BAK complex / positive regulation of reproductive process / positive regulation of mitochondrial membrane permeability involved in apoptotic process ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / B cell negative selection / BAK complex / positive regulation of reproductive process / positive regulation of mitochondrial membrane permeability involved in apoptotic 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 / apoptotic process involved in blood vessel morphogenesis / NTRK3 as a dependence receptor / negative regulation of endoplasmic reticulum calcium ion concentration / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / glycosphingolipid metabolic process / Release of apoptotic factors from the mitochondria / B cell homeostatic proliferation / apoptotic process involved in embryonic digit morphogenesis / retinal cell programmed cell death / post-embryonic camera-type eye morphogenesis / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / mitochondrial fragmentation involved in apoptotic process / establishment or maintenance of transmembrane electrochemical gradient / mitochondrial permeability transition pore complex / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / B cell apoptotic process / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / fertilization / calcium ion transport into cytosol / myeloid cell homeostasis / Bcl-2 family protein complex / mitochondrial fusion / positive regulation of epithelial cell apoptotic process / motor neuron apoptotic process / BH domain binding / epithelial cell apoptotic process / thymocyte apoptotic process / execution phase of apoptosis / positive regulation of calcium ion transport into cytosol / hypothalamus development / pore complex / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / negative regulation of peptidyl-serine phosphorylation / B cell homeostasis / vagina development / BH3 domain binding / germ cell development / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / apoptotic mitochondrial changes / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / ectopic germ cell programmed cell death / Pyroptosis / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / cellular response to unfolded protein / response to axon injury / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / negative regulation of fibroblast proliferation / supramolecular fiber organization / homeostasis of number of cells within a tissue / response to salt stress / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway / Hsp70 protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / kidney development / regulation of mitochondrial membrane potential / apoptotic signaling pathway / negative regulation of protein binding / response to gamma radiation / positive regulation of protein-containing complex assembly / neuron migration / cellular response to virus / cerebral cortex development / response to toxic substance / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / cellular response to UV / channel activity
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 ...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 / BCL2-like apoptosis inhibitors family profile. / Apoptosis regulator proteins, Bcl-2 family / Bcl-2-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMiller, 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: 2024
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 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,94412
Polymers35,8854
Non-polymers1,0598
Water36020
1
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4556
Polymers17,9422
Non-polymers5134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-28 kcal/mol
Surface area9180 Å2
MethodPISA
2
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4896
Polymers17,9422
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.393, 67.393, 140.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-313-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 8971.242 Da / Num. of mol.: 4 / Mutation: C62S, D71N, C126S
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 , 5 types, 28 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953651 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953651 Å / Relative weight: 1
ReflectionResolution: 2.25→44.93 Å / Num. obs: 18223 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.164 / Net I/σ(I): 11.43
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.25-2.392.70728670.3682.8481
2.39-2.551.60727260.6371.6911
2.55-2.750.9925260.8221.0451
2.75-3.020.56523600.9290.5951
3.02-3.370.28921490.9810.3051
3.37-3.890.13818900.9950.1451
3.89-4.750.0716250.9980.0741
4.75-6.690.06813020.9980.0711
6.69-44.930.0377810.0321

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.93 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 912 5.01 %
Rwork0.2543 --
obs0.2559 18217 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 69 20 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022419
X-RAY DIFFRACTIONf_angle_d0.4523223
X-RAY DIFFRACTIONf_dihedral_angle_d14.308898
X-RAY DIFFRACTIONf_chiral_restr0.031354
X-RAY DIFFRACTIONf_plane_restr0.003406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.35691270.33732399X-RAY DIFFRACTION100
2.37-2.520.37161270.33212424X-RAY DIFFRACTION100
2.52-2.710.30181300.28252456X-RAY DIFFRACTION100
2.71-2.980.3361280.28492427X-RAY DIFFRACTION100
2.98-3.420.31611300.27972474X-RAY DIFFRACTION100
3.42-4.30.26021310.22882489X-RAY DIFFRACTION100
4.3-44.930.26161390.23172636X-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)
14.4232-3.7004-2.72364.39095.94110.0304-0.3986-0.5260.7838-0.59361.1215-0.9462-0.37370.8804-0.50010.69290.04950.13050.5657-0.12070.723218.4008-16.088644.3517
27.6805-3.2557-3.30544.85974.97538.48350.0164-0.1718-0.00450.5789-0.1816-0.0394-0.15150.4933-0.41870.49050.1582-0.01530.47360.11360.784123.1611-26.855838.516
35.9113.7662-1.62726.15-1.6423.5741-0.0459-0.0939-1.17220.3647-0.0852-1.02180.38550.44620.14330.26610.05780.01430.51580.0290.531314.8961-25.00333.9033
46.19913.82890.10935.0966-2.44043.35130.05181.34940.4218-0.610.14991.3595-0.3608-0.6524-0.49110.52560.0493-0.04080.4839-0.00340.6151-14.5738.7664.4406
52.60273.1712-0.30798.4275-1.62212.66840.1845-0.526-0.3318-0.63470.75391.20870.8702-1.4018-0.78920.4514-0.0016-0.04450.80140.12890.8784-24.9576-3.93817.4777
67.0813-0.5752-1.32253.2842.1785.5154-0.7429-1.2288-1.50731.3348-0.21980.03971.20160.75480.34110.66490.0020.08530.5550.21951.0042-13.8826-8.997426.791
77.8546-1.06713.39445.3599-3.03756.2634-0.66571.3635-1.26571.00333.16610.12511.12822.55440.39370.69470.3326-0.16740.68680.07320.8948-6.2805-11.09111.6073
84.5621-2.0041-1.39222.59741.24778.125-0.0904-0.71140.8667-0.17030.4949-0.2312-0.33940.80490.38170.4298-0.038-0.17810.4369-0.00380.6167-14.0680.234820.3956
94.5351-0.1162-8.44745.0485-0.72177.3428-0.63710.2535-1.0577-0.34650.38220.67041.7058-0.28970.44780.4766-0.0047-0.07830.49860.00590.7709-16.675-8.897311.3848
103.97460.9295-0.27213.38352.88393.078-0.30311.6459-0.4537-1.67390.2264-0.74460.430.1027-0.12940.65130.04410.05440.5077-0.05240.5583-4.53324.47281.6513
119.7666-6.85164.99131.9635-9.76088.9041-1.34825.92884.4460.1724-1.8631-8.2437-1.23322.17092.88381.32420.16350.0921.6370.77232.6333.441616.38194.4507
123.3749-1.2396-0.67223.10340.6874.91490.67330.49990.8214-0.8379-1.0282-0.5278-0.69420.05650.27130.7654-0.0680.03940.51730.10931.1708-8.383518.49128.8369
134.6484-0.60662.68355.2388-2.41742.6043-0.401-3.49211.93092.93130.62132.5691-2.6394-1.6817-0.58430.69090.3154-0.16070.307-0.30771.2249-21.378114.919411.2538
142.12790.54710.24042.39411.51714.120.2148-0.30050.06880.02130.0467-0.33070.2320.2501-0.13820.4751-0.0311-0.06430.34820.00790.575-5.24068.847413.3886
155.76472.64914.9014.6158-0.48246.47891.0165-2.3127-1.69281.25220.24920.03180.6391-1.3182-0.84610.65820.12720.07840.50250.05790.780110.4616-28.233441.544
164.71770.6593.743.16541.58674.81060.7388-1.81490.1140.3371-1.02441.48121.7986-3.76520.26170.6089-0.1034-0.05840.70750.24561.481-4.9157-31.961430.2715
175.75670.91690.93632.90550.76679.96140.27970.2183-0.5926-0.24430.13451.1663-0.1678-1.51-0.06530.54850.0711-0.04610.93620.31380.7463-5.512-20.125321.2522
185.34632.72624.76887.34820.14667.2375-0.15780.0363-0.23530.24250.31070.3164-0.01440.0546-0.0170.17120.02450.08860.35510.10340.4613.15-22.554625.9489
196.7815-0.62981.18286.23256.54936.6176-0.2407-0.37950.49660.7185-0.16721.73340.0163-2.03870.8970.4978-0.01010.11050.74840.20190.7642-3.9646-21.053633.9362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 72 through 86 )
2X-RAY DIFFRACTION2chain 'D' and (resid 87 through 100 )
3X-RAY DIFFRACTION3chain 'D' and (resid 101 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 81 )
6X-RAY DIFFRACTION6chain 'A' and (resid 82 through 98 )
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 106 )
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 54 through 73 )
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 87 )
12X-RAY DIFFRACTION12chain 'B' and (resid 88 through 100 )
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 106 )
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 126 )
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 72 )
16X-RAY DIFFRACTION16chain 'C' and (resid 73 through 81 )
17X-RAY DIFFRACTION17chain 'C' and (resid 82 through 101 )
18X-RAY DIFFRACTION18chain 'C' and (resid 102 through 127 )
19X-RAY DIFFRACTION19chain 'D' and (resid 53 through 71 )

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