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- PDB-5w60: Crystal structure of BAXP168G monomer cryo-protected with ethylen... -

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Basic information

Entry
Database: PDB / ID: 5w60
TitleCrystal structure of BAXP168G monomer cryo-protected with ethylene glycol
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 / BAX complex / protein insertion into mitochondrial membrane / 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 / Activation, translocation and oligomerization of BAX ...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 / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / positive regulation of B cell apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / glycosphingolipid metabolic process / retinal cell programmed cell death / B cell negative selection / BAK complex / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / Transcriptional regulation by RUNX2 / 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 / endoplasmic reticulum calcium ion homeostasis / positive regulation of epithelial cell apoptotic process / fertilization / calcium ion transport into cytosol / epithelial cell apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / motor neuron apoptotic process / execution phase of apoptosis / thymocyte apoptotic process / pore complex / hypothalamus development / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / BH3 domain binding / vagina development / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / B cell homeostasis / positive regulation of calcium ion transport into cytosol / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / ectopic germ cell programmed cell death / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of protein binding / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / extrinsic apoptotic signaling pathway / response to salt stress / release of sequestered calcium ion into cytosol / Hsp70 protein binding / extrinsic apoptotic signaling pathway in absence of ligand / homeostasis of number of cells within a tissue / 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 / response to gamma radiation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / kidney development / positive regulation of protein-containing complex assembly / cerebral cortex development / cellular response to virus / response to toxic substance / neuron migration / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / nuclear envelope / positive regulation of neuron apoptotic process / retina development in camera-type eye / channel activity / regulation of apoptotic process
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsRobin, A.Y. / Colman, P.M. / Czabotar, P.E.
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)21,4022
Polymers21,3061
Non-polymers961
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-9 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.719, 50.716, 64.413
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 / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 21306.316 Da / Num. of mol.: 1 / Mutation: C62S C126S P168G
Source method: isolated from a genetically manipulated source
Details: Two additional serine residues at C-terminus due to cloning strategy.
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.68 Å3/Da / Density % sol: 26.69 %
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: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.803→36.174 Å / Num. obs: 13738 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07706 / Net I/σ(I): 16.9
Reflection shellHighest resolution: 1.803 Å / Rmerge(I) obs: 0.8226 / CC1/2: 0.796

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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

4bd2


Resolution: 1.803→36.174 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.36
RfactorNum. reflection% reflection
Rfree0.2385 688 5.01 %
Rwork0.1931 --
obs0.1953 13738 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.803→36.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 5 96 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061447
X-RAY DIFFRACTIONf_angle_d0.7811969
X-RAY DIFFRACTIONf_dihedral_angle_d12.606859
X-RAY DIFFRACTIONf_chiral_restr0.044224
X-RAY DIFFRACTIONf_plane_restr0.005248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8028-1.9420.32091350.23862561X-RAY DIFFRACTION100
1.942-2.13740.28081350.20892557X-RAY DIFFRACTION100
2.1374-2.44660.26861360.19472586X-RAY DIFFRACTION100
2.4466-3.08230.27171380.19482611X-RAY DIFFRACTION100
3.0823-36.1810.19371440.18142735X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -8.0742 Å / Origin y: -0.2681 Å / Origin z: 10.3055 Å
111213212223313233
T0.1112 Å20.0312 Å20.0146 Å2-0.1134 Å20.0164 Å2--0.1044 Å2
L0.5915 °2-0.1017 °2-0.0937 °2-0.6134 °2-0.087 °2--0.9052 °2
S-0.0012 Å °0.0741 Å °0.022 Å °-0.0536 Å °-0.0047 Å °-0.0432 Å °-0.1098 Å °-0.1724 Å °-0.0207 Å °
Refinement TLS groupSelection details: chain A

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