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- PDB-8g1t: Crystal structure of Bax core domain BH3-groove dimer - tetrameri... -

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Basic information

Entry
Database: PDB / ID: 8g1t
TitleCrystal structure of Bax core domain BH3-groove dimer - tetrameric fraction P21
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
Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsCowan, A.D. / Colman, P.M. / Czabotar, P.E. / Miller, M.S.
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
DepositionFeb 2, 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
E: Apoptosis regulator BAX
F: Apoptosis regulator BAX
G: Apoptosis regulator BAX
H: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8409
Polymers71,7788
Non-polymers621
Water99155
1
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)17,9442
Polymers17,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-32 kcal/mol
Surface area8260 Å2
MethodPISA
2
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)17,9442
Polymers17,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-29 kcal/mol
Surface area8060 Å2
MethodPISA
3
E: Apoptosis regulator BAX
F: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0073
Polymers17,9442
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-29 kcal/mol
Surface area8300 Å2
MethodPISA
4
G: Apoptosis regulator BAX
H: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)17,9442
Polymers17,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-30 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.363, 70.374, 62.784
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 8972.228 Da / Num. of mol.: 8
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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 1.86 Å3/Da / Density % sol: 33.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.44 M sodium citrate, 0.01 M TCEP

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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 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.09→46.85 Å / Num. obs: 30887 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.071 / Rrim(I) all: 0.136 / Net I/σ(I): 8.4 / Num. measured all: 112776
Reflection shellResolution: 2.09→2.15 Å / % possible obs: 94.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 1.829 / Num. measured all: 8390 / Num. unique obs: 2408 / CC1/2: 0.269 / Rpim(I) all: 1.125 / Rrim(I) all: 2.152 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIXv1.13refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.092→45.817 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 2029 6.58 %
Rwork0.2049 --
obs0.2079 30813 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.092→45.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 4 55 4513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084529
X-RAY DIFFRACTIONf_angle_d1.0126073
X-RAY DIFFRACTIONf_dihedral_angle_d12.5362742
X-RAY DIFFRACTIONf_chiral_restr0.056676
X-RAY DIFFRACTIONf_plane_restr0.007773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0923-2.14460.38281370.37831867X-RAY DIFFRACTION91
2.1446-2.20260.36921330.33082069X-RAY DIFFRACTION100
2.2026-2.26740.33961420.32252052X-RAY DIFFRACTION99
2.2674-2.34060.35211480.30592054X-RAY DIFFRACTION100
2.3406-2.42420.39311570.27672091X-RAY DIFFRACTION100
2.4242-2.52130.27751300.25152063X-RAY DIFFRACTION100
2.5213-2.6360.30121520.23622067X-RAY DIFFRACTION100
2.636-2.7750.2831450.2242053X-RAY DIFFRACTION100
2.775-2.94880.28331480.22222092X-RAY DIFFRACTION100
2.9488-3.17640.2521490.20352075X-RAY DIFFRACTION100
3.1764-3.4960.28811340.19712094X-RAY DIFFRACTION100
3.496-4.00160.18391480.1692070X-RAY DIFFRACTION99
4.0016-5.04060.1991470.15372071X-RAY DIFFRACTION99
5.0406-45.8170.20991590.18182066X-RAY DIFFRACTION97
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)
18.21424.8339-1.43382.9257-1.63085.9624-0.2275-0.41140.0141-1.06670.63761.68560.1043-0.5945-0.45740.42770.0143-0.18370.53320.11640.552935.409534.948354.9399
28.7186-0.91623.68677.8594-4.02044.72-0.158-0.45950.93740.4079-0.12620.2776-0.70520.12150.16840.4406-0.0088-0.0150.4502-0.16070.418349.840652.793562.3054
32.77332.8852-1.66163.241-2.93117.7807-0.2091-0.2414-0.1394-0.4011-0.0890.0743-0.0712-0.74250.0620.41360.0069-0.12280.40030.05120.387350.565345.341658.2175
42.91822.34511.75986.46490.53174.09320.2357-0.7641.03381.517-0.25262.03210.2363-0.65190.1680.43160.02440.14560.7251-0.07980.812941.997649.527665.482
57.4594-3.65643.2772.2132-0.7683.9784-0.32910.7918-0.48930.61480.15821.07880.1389-0.73451.30320.675-0.16380.21490.71510.23050.611837.655127.22864.983
63.873-4.36730.48347.2845-3.58343.855-0.62010.7689-1.06390.034-0.3421-0.67280.7509-0.2223-0.19510.48610.03-0.02740.23090.12720.753143.60923.793352.9152
76.15114.07880.20767.53324.05344.09-0.08910.1856-0.2080.06340.03540.1517-0.56530.28840.28590.3321-0.0096-0.07560.25030.08640.383744.266833.792254.3866
83.81212.27034.32217.74952.81725.3798-0.52090.3914-0.0378-0.27850.2015-1.6852-0.38042.27410.45180.61210.1026-0.00620.5859-0.04990.6168.948839.959761.8193
93.43843.8842-1.05118.68831.52355.8942-0.3880.4683-0.0545-0.90180.6747-0.2439-0.33680.053-0.36570.5634-0.0759-0.0340.42580.01020.395255.966230.018244.9568
106.4773-5.06312.78228.5231-5.51775.9967-0.0810.32780.3851-0.5470.4051-0.0551-0.76580.4857-0.33510.4891-0.1105-0.04150.260.09870.322254.690335.157651.5569
115.10370.77596.25913.03241.96228.41031.09721.3141-0.54070.3894-0.1761-1.65011.48931.7653-0.45420.5329-0.1838-0.06740.74460.05350.602262.82427.150250.283
129.5512-3.4187-6.77054.90490.7365.6330.0537-2.11020.96220.60070.6363-1.59180.61380.87710.32381.00150.02-0.39270.67750.09320.785865.637132.953571.6575
134.34111.7768-4.56613.5108-3.43395.72030.3172-1.03430.55340.84560.4372-0.5876-0.23970.354-0.61040.5222-0.0394-0.01750.4282-0.07210.422460.91145.675970.7376
145.9015-1.13831.94378.93163.31756.1692-0.0949-0.4717-0.09120.30120.4085-0.2984-0.1928-0.054-0.20230.27780.0373-0.08160.2820.00010.239259.97141.105162.9661
154.0344-0.6377-2.61256.63893.57844.4395-0.7215-1.51510.8920.98540.41110.09010.07230.0320.19370.59620.0444-0.06270.28670.0480.439729.809122.62240.7661
163.2806-3.9742-3.94926.48986.06287.28730.0765-0.30580.5926-0.09650.8496-1.2555-0.26952.2158-1.05840.5529-0.1065-0.17050.6214-0.07860.789451.219417.780437.0426
176.79375.92550.7077.99-2.52997.86380.06150.9014-0.3685-0.78850.4147-1.6181.09440.32050.00610.34070.03350.06520.5055-0.17670.866450.23269.536925.7781
187.1207-3.2896-0.14286.23431.11777.38630.06840.3137-0.05920.6430.1991-0.2771-0.11740.5718-0.23420.3392-0.0801-0.1020.2816-0.01540.351641.366612.780728.8202
192.67452.55233.35536.3552-0.32937.44480.5851-0.3123-0.04251.03870.0981-0.22650.17250.5688-0.53680.60070.0187-0.0490.2973-0.03960.613641.31958.534937.0035
208.0162-3.0293-1.22014.0063-2.97244.1523-0.18660.3367-0.5190.48640.49950.7610.2992-0.9191-0.43020.4376-0.11470.00440.3256-0.04870.487321.154720.841733.2237
216.6955-2.1879-1.04194.547-0.50878.47-0.56520.3558-0.188-0.95850.03480.8438-0.0023-0.26290.27080.2353-0.0267-0.02510.1811-0.00510.33829.513922.244930.764
228.13911.77910.73037.5325.83719.0328-0.1011.16870.2877-3.12150.5542-0.7645-0.89361.0069-0.6280.3934-0.06030.04770.58960.01850.454241.995815.8299.0713
236.5313-3.101-1.15423.84466.07692.0126-1.29391.37650.6951-2.76420.20320.0401-2.4271-0.64990.01570.9244-0.27940.22730.62880.20660.800741.681635.566514.7644
243.31563.50070.52666.36833.52963.50370.2925-0.19230.7768-0.2156-0.0316-0.2528-0.766-0.32990.09740.59950.0435-0.04730.273-0.0630.613331.625436.603526.0138
258.88281.13230.28667.72570.96719.16240.1240.34320.1442-0.4516-0.20270.2106-0.3014-0.05580.11120.3209-0.02620.0230.17590.01340.326632.326726.547321.3305
267.17742.5796-1.33823.0026-2.90873.003-1.07521.26070.3989-3.00511.06371.2412-1.61190.1138-0.1331.0219-0.2644-0.07780.54690.12070.486530.726829.578412.6903
279.9081-7.71245.45766.6474-3.86493.280.7316-0.0237-0.6129-0.92920.04091.03060.4839-0.5661-0.94540.7039-0.0029-0.09110.7203-0.21330.640732.06647.36489.8028
287.48555.17822.61428.9243-0.13132.51290.23640.0807-0.1799-1.3904-0.5252-0.82610.28360.62580.13740.3505-0.01540.18630.4330.03650.656545.67789.360116.6216
297.7863-1.8371.78236.09371.16867.3838-0.0199-0.34330.3497-0.2212-0.01330.65710.0511-0.62380.02750.28850.00780.02070.2107-0.01990.347333.503812.621419.6371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 124 )
4X-RAY DIFFRACTION4chain 'B' and (resid 54 through 72 )
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 99 )
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 122 )
8X-RAY DIFFRACTION8chain 'C' and (resid 54 through 72 )
9X-RAY DIFFRACTION9chain 'C' and (resid 73 through 106 )
10X-RAY DIFFRACTION10chain 'C' and (resid 107 through 123 )
11X-RAY DIFFRACTION11chain 'D' and (resid 54 through 72 )
12X-RAY DIFFRACTION12chain 'D' and (resid 73 through 87 )
13X-RAY DIFFRACTION13chain 'D' and (resid 88 through 99 )
14X-RAY DIFFRACTION14chain 'D' and (resid 100 through 124 )
15X-RAY DIFFRACTION15chain 'E' and (resid 55 through 72 )
16X-RAY DIFFRACTION16chain 'E' and (resid 73 through 87 )
17X-RAY DIFFRACTION17chain 'E' and (resid 88 through 99 )
18X-RAY DIFFRACTION18chain 'E' and (resid 100 through 123 )
19X-RAY DIFFRACTION19chain 'F' and (resid 56 through 72 )
20X-RAY DIFFRACTION20chain 'F' and (resid 73 through 99 )
21X-RAY DIFFRACTION21chain 'F' and (resid 100 through 126 )
22X-RAY DIFFRACTION22chain 'G' and (resid 54 through 72 )
23X-RAY DIFFRACTION23chain 'G' and (resid 73 through 82 )
24X-RAY DIFFRACTION24chain 'G' and (resid 83 through 99 )
25X-RAY DIFFRACTION25chain 'G' and (resid 100 through 124 )
26X-RAY DIFFRACTION26chain 'H' and (resid 55 through 72 )
27X-RAY DIFFRACTION27chain 'H' and (resid 73 through 87 )
28X-RAY DIFFRACTION28chain 'H' and (resid 88 through 106 )
29X-RAY DIFFRACTION29chain 'H' and (resid 107 through 128 )

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