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- PDB-6eb6: Crystal structure of BAX W139A monomer -

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Basic information

Entry
Database: PDB / ID: 6eb6
TitleCrystal structure of BAX W139A monomer
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / BAX / inactive monomer
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
FORMIC ACID / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.023 Å
AuthorsRobin, A.Y.
CitationJournal: Cell Rep / Year: 2019
Title: BAX Activation: Mutations Near Its Proposed Non-canonical BH3 Binding Site Reveal Allosteric Changes Controlling Mitochondrial Association.
Authors: Dengler, M.A. / Robin, A.Y. / Gibson, L. / Li, M.X. / Sandow, J.J. / Iyer, S. / Webb, A.I. / Westphal, D. / Dewson, G. / Adams, J.M.
History
DepositionAug 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2735
Polymers21,0891
Non-polymers1844
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.159, 63.159, 82.265
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 21089.225 Da / Num. of mol.: 1 / Mutation: W139A
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-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium formate, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.023→45.55 Å / Num. obs: 12611 / % possible obs: 98.4 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06257 / Net I/σ(I): 21.15
Reflection shellResolution: 2.023→2.095 Å / Rmerge(I) obs: 0.5258 / Num. unique obs: 1200 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W61

5w61


Resolution: 2.023→32.87 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.2013 630 5 %
Rwork0.1714 --
obs0.1729 12607 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.023→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 12 58 1442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071464
X-RAY DIFFRACTIONf_angle_d0.7341985
X-RAY DIFFRACTIONf_dihedral_angle_d19.651870
X-RAY DIFFRACTIONf_chiral_restr0.044226
X-RAY DIFFRACTIONf_plane_restr0.005253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0227-2.22630.25071510.19682894X-RAY DIFFRACTION97
2.2263-2.54840.22871590.18162956X-RAY DIFFRACTION98
2.5484-3.21060.20791570.18122987X-RAY DIFFRACTION98
3.2106-45.55970.18481630.16133140X-RAY DIFFRACTION99
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)
17.16090.1284-3.57563.05482.18184.25460.14660.330.23320.1828-0.1174-0.0247-0.036-0.7076-0.06390.2872-0.0307-0.02130.2310.03350.253620.3269-14.4615-2.225
24.5617-2.1678-4.93866.35860.93565.7911-0.68860.2404-1.1711-0.9250.05260.53431.11630.2840.56360.6903-0.04350.10210.4952-0.04620.448618.7854-21.8817-8.4619
37.30845.0303-5.74584.8984-5.29277.0634-0.52381.5910.3658-0.30530.64440.3488-0.6295-0.6194-0.11250.6082-0.0922-0.08780.38580.02330.318322.7248-5.5093-7.5716
44.24582.3867-1.15467.6793-3.27568.13760.0088-0.354-0.3985-0.3709-0.0013-0.44820.29931.11820.03030.2806-0.00740.04140.3769-0.02060.283840.009-13.0254-0.2516
59.1093-3.50017.69861.3596-2.9986.6145-0.6976-1.54361.46070.6490.6914-1.5911-0.8908-0.33930.27020.4092-0.0551-0.15370.4842-0.1390.49831.9935-3.530211.4026
62.5734-2.653-2.52687.30575.78096.66860.05740.17030.0328-0.83820.097-0.0638-0.31850.2954-0.17470.3866-0.03920.04120.27710.04360.268231.7192-13.45-3.065
77.6603-3.5263-5.15994.70243.97414.3324-0.52830.1094-0.71430.2447-0.03310.64640.7402-0.14280.49290.43310.00450.04120.31480.0810.295928.6392-21.48713.3976
87.34823.1480.88857.2437-2.44117.7367-0.2368-0.47110.5844-0.1284-0.20470.4825-0.6882-0.40240.35360.34660.0369-0.0260.2234-0.0630.31220.3014-3.79077.8257
95.52212.7628-2.06256.83631.94156.1514-0.3536-0.29180.0196-0.89010.34160.4622-0.69440.05180.1640.4829-0.1307-0.06880.28890.01270.248335.5141-1.5589-1.4063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 72 )
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 127 )
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 147 )
8X-RAY DIFFRACTION8chain 'A' and (resid 148 through 164 )
9X-RAY DIFFRACTION9chain 'A' and (resid 165 through 191 )

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