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- PDB-4bd6: Bax domain swapped dimer in complex with BaxBH3 -

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Basic information

Entry
Database: PDB / ID: 4bd6
TitleBax domain swapped dimer in complex with BaxBH3
Components(APOPTOSIS REGULATOR BAX) x 2
KeywordsAPOPTOSIS / PROGRAMMED CELL DEATH
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
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 / BCL2-like apoptosis inhibitors family profile. / Apoptosis regulator proteins, Bcl-2 family / 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: 2.494 Å
AuthorsCzabotar, P.E. / Westphal, D. / Adams, J.M. / Colman, P.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Bax Crystal Structures Reveal How Bh3 Domains Activate Bax and Nucleate its Oligomerization to Induce Apoptosis.
Authors: Czabotar, P.E. / Westphal, D. / Dewson, G. / Ma, S. / Hockings, C. / Fairlie, W.D. / Lee, E.F. / Yao, S. / Robin, A.Y. / Smith, B.J. / Huang, D.C. / Kluck, R.M. / Adams, J.M. / Colman, P.M.
History
DepositionOct 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APOPTOSIS REGULATOR BAX
C: APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)23,0202
Polymers23,0202
Non-polymers00
Water1629
1
A: APOPTOSIS REGULATOR BAX
C: APOPTOSIS REGULATOR BAX

A: APOPTOSIS REGULATOR BAX
C: APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)46,0404
Polymers46,0404
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10370 Å2
ΔGint-116.4 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.715, 103.715, 40.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein APOPTOSIS REGULATOR BAX / BCL-2-LIKE PROTEIN 4 / BCL2-L-4


Mass: 19182.711 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-171 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q07812
#2: Protein/peptide APOPTOSIS REGULATOR BAX / BCL-2-LIKE PROTEIN 4 / BCL2-L-4


Mass: 3837.381 Da / Num. of mol.: 1 / Fragment: RESIDUES 48-81 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q07812
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.37 Å3/Da / Density % sol: 48.1 % / Description: NONE
Crystal growDetails: 1.4 M SODIUM CITRATE, 0.1 M SODIUM CACODYLATE PH 5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→51.8 Å / Num. obs: 8067 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 72.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.72
Reflection shellResolution: 2.49→2.85 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.693 / Mean I/σ(I) obs: 1.45 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BAX DOMAIN SWAPPED DIMER INDUCED BY OCTYLMALTOSIDE

Resolution: 2.494→51.858 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 404 5 %
Rwork0.2463 --
obs0.2482 8067 98.98 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.462 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 83.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.0606 Å20 Å20 Å2
2---0.0606 Å20 Å2
3---0.1213 Å2
Refinement stepCycle: LAST / Resolution: 2.494→51.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 0 9 1314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121326
X-RAY DIFFRACTIONf_angle_d1.481781
X-RAY DIFFRACTIONf_dihedral_angle_d15.174493
X-RAY DIFFRACTIONf_chiral_restr0.078197
X-RAY DIFFRACTIONf_plane_restr0.008227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4938-2.85460.37991300.31832444X-RAY DIFFRACTION97
2.8546-3.59640.30181330.25472538X-RAY DIFFRACTION100
3.5964-51.86870.26871410.23472681X-RAY DIFFRACTION100

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