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- PDB-4bd8: Bax domain swapped dimer induced by BimBH3 with CHAPS -

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Basic information

Entry
Database: PDB / ID: 4bd8
TitleBax domain swapped dimer induced by BimBH3 with CHAPS
ComponentsAPOPTOSIS REGULATOR BAX
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 / 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 / NTRK3 as a dependence receptor / 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 / 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 / Transcriptional regulation by RUNX2 / 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 endoplasmic reticulum unfolded protein response / fertilization / calcium ion transport into cytosol / channel activity / motor neuron 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 / 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 / positive regulation of IRE1-mediated unfolded protein response / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / negative regulation of apoptotic signaling pathway / B cell homeostasis / 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 / blood vessel remodeling / ectopic germ cell programmed cell death / cellular response to unfolded protein / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / 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 / 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 / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to gamma radiation / neuron migration / cerebral cortex development / response to toxic substance / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage
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
PRASEODYMIUM ION / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,50914
Polymers76,7314
Non-polymers77810
Water4,071226
1
A: APOPTOSIS REGULATOR BAX
B: APOPTOSIS REGULATOR BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,08211
Polymers38,3652
Non-polymers7169
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-78.1 kcal/mol
Surface area14770 Å2
MethodPISA
2
C: APOPTOSIS REGULATOR BAX
D: APOPTOSIS REGULATOR BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4273
Polymers38,3652
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-82.8 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.947, 142.947, 86.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

21A-2017-

HOH

31A-2029-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6252, 0.2398, 0.7427), (0.2367, -0.9651, 0.1124), (0.7437, 0.1055, -0.6601)-27.027, 49.8599, 42.9004
2given(0.5632, -0.3418, -0.7523), (0.8234, 0.1556, 0.5457), (-0.0695, -0.9268, 0.3691)34.8819, 19.2972, 7.8303
3given(0.4275, -0.8991, 0.0942), (-0.6508, -0.3785, -0.6582), (0.6274, 0.2201, -0.7469)-4.6998, 41.7901, 70.7836

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Components

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


Mass: 19182.711 Da / Num. of mol.: 4 / 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: Chemical ChemComp-PR / PRASEODYMIUM ION / Praseodymium


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.96 Å3/Da / Density % sol: 58.49 % / Description: NONE
Crystal growDetails: 1.8 M NH4SO4, 0.1 M HEPES PH 6.5, 10 MM PRCL3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.22→19.82 Å / Num. obs: 32132 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 93.5 % / Biso Wilson estimate: 46.17 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.55
Reflection shellResolution: 2.22→2.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.9 / % possible all: 93.5

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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: 2.22→19.823 Å / SU ML: 0.41 / σ(F): 1.99 / Phase error: 33.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 1607 5 %
Rwork0.1972 --
obs0.2003 32132 98.53 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.95 Å2
Refinement stepCycle: LAST / Resolution: 2.22→19.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 34 226 4664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084520
X-RAY DIFFRACTIONf_angle_d1.0686095
X-RAY DIFFRACTIONf_dihedral_angle_d14.1451597
X-RAY DIFFRACTIONf_chiral_restr0.071677
X-RAY DIFFRACTIONf_plane_restr0.004766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2203-2.29180.56871340.52152549X-RAY DIFFRACTION89
2.2918-2.37360.33981430.31562720X-RAY DIFFRACTION98
2.3736-2.46850.27361480.23352810X-RAY DIFFRACTION100
2.4685-2.58060.26781490.21692837X-RAY DIFFRACTION100
2.5806-2.71630.27471480.20422795X-RAY DIFFRACTION100
2.7163-2.8860.30891480.2022825X-RAY DIFFRACTION100
2.886-3.10810.25331480.20622810X-RAY DIFFRACTION100
3.1081-3.41940.25041480.19552807X-RAY DIFFRACTION100
3.4194-3.91090.25281470.17322803X-RAY DIFFRACTION100
3.9109-4.91490.20521490.15872827X-RAY DIFFRACTION100
4.9149-19.8240.2421450.18042742X-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)
11.3801-0.7482-0.59522.6948-0.13411.94580.0430.06-0.1515-0.1487-0.02480.22980.053-0.0572-00.33720.0168-0.06110.37440.01540.5579-18.7123.14217.9015
21.3460.5507-0.31631.6882-0.01554.31790.252-0.01190.0477-0.1050.0283-0.0079-0.29460.08730.00040.48110.03060.01510.41220.00690.3017-23.860144.081316.7258
31.1220.48871.46382.52841.66441.99010.02490.2201-0.26750.2935-0.0919-0.21040.5040.0735-0.04290.65760.06810.0410.4765-0.05360.5218-28.796211.170149.5806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:129) OR CHAIN B AND (RESSEQ 130:170)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 1:129) OR CHAIN A AND (RESSEQ 130:170)
3X-RAY DIFFRACTION3CHAIN C OR CHAIN D

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