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- PDB-5w62: Crystal structure of mouse BAX monomer -

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Basic information

Entry
Database: PDB / ID: 5w62
TitleCrystal structure of mouse BAX monomer
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / BAX / monomer / mouse
Function / homology
Function and homology information


outer mitochondrial membrane organization / Activation, translocation and oligomerization of BAX / positive regulation of developmental process / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / leukocyte homeostasis / Pyroptosis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation ...outer mitochondrial membrane organization / Activation, translocation and oligomerization of BAX / positive regulation of developmental process / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / leukocyte homeostasis / Pyroptosis / 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 / inner mitochondrial membrane organization / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / positive regulation of B cell apoptotic process / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / 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 / BH domain binding / 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 / sex differentiation / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / limb morphogenesis / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / cellular respiration / calcium ion transport into cytosol / channel activity / motor neuron apoptotic process / regulation of mitochondrial membrane permeability involved in apoptotic process / mitochondrial fusion / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / epithelial cell apoptotic process / hypothalamus development / positive regulation of calcium ion transport into cytosol / response to ionizing radiation / cellular response to organic substance / thymocyte apoptotic process / pore complex / BH3 domain binding / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / germ cell development / negative regulation of mitochondrial membrane potential / positive regulation of release of cytochrome c from mitochondria / vagina development / negative regulation of apoptotic signaling pathway / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / homeostasis of number of cells / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / blood vessel remodeling / ectopic germ cell programmed cell death / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / regulation of neuron apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / heat shock protein binding / mitochondrion organization / intrinsic apoptotic signaling pathway / post-embryonic development / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / negative regulation of protein binding / epithelial cell proliferation / kidney development / cell periphery / establishment of localization in cell
Similarity search - Function
Blc2-like / Apoptosis Regulator Bcl-x / 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 ...Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator BAX
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsRobin, A.Y. / Colman, P.M. / Czabotar, P.E. / Luo, C.S.
CitationJournal: Structure / Year: 2018
Title: Ensemble Properties of Bax Determine Its Function.
Authors: Robin, A.Y. / Iyer, S. / Birkinshaw, R.W. / Sandow, J. / Wardak, A. / Luo, C.S. / Shi, M. / Webb, A.I. / Czabotar, P.E. / Kluck, R.M. / Colman, P.M.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Oct 4, 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

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Assembly

Deposited unit
A: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4772
Polymers21,3811
Non-polymers961
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.787, 51.950, 62.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apoptosis regulator BAX


Mass: 21381.400 Da / Num. of mol.: 1 / Mutation: C62S C126S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bax / Production host: Escherichia coli (E. coli) / References: UniProt: Q07813
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.56 Å3/Da / Density % sol: 21.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.196→34.236 Å / Num. obs: 7218 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0685 / Net I/σ(I): 18.44
Reflection shellHighest resolution: 2.196 Å / Rmerge(I) obs: 0.9765 / CC1/2: 0.695

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BD2, 5W60

4bd2

5w60


Resolution: 2.196→34.236 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.29
RfactorNum. reflection% reflection
Rfree0.2842 722 10 %
Rwork0.2082 --
obs0.216 7218 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.196→34.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 5 26 1237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061236
X-RAY DIFFRACTIONf_angle_d0.7471677
X-RAY DIFFRACTIONf_dihedral_angle_d10.999710
X-RAY DIFFRACTIONf_chiral_restr0.043193
X-RAY DIFFRACTIONf_plane_restr0.005206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1962-2.36570.31941410.24591268X-RAY DIFFRACTION100
2.3657-2.60370.33021420.24141274X-RAY DIFFRACTION100
2.6037-2.98030.32671400.2351272X-RAY DIFFRACTION100
2.9803-3.75410.31331450.20581310X-RAY DIFFRACTION100
3.7541-34.23980.24741540.19121372X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.1366 Å / Origin y: -0.6044 Å / Origin z: -13.1954 Å
111213212223313233
T0.2872 Å2-0.0409 Å2-0.0306 Å2-0.273 Å2-0.0087 Å2--0.2873 Å2
L1.7039 °2-0.8979 °20.2803 °2-2.6925 °2-1.6853 °2--2.8669 °2
S0.1709 Å °-0.0931 Å °0.0295 Å °-0.143 Å °0.0827 Å °0.1795 Å °0.1424 Å °0.0008 Å °0.0044 Å °
Refinement TLS groupSelection details: chain 'A'

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