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- PDB-4s0o: Crystal Structure of the Autoinhibited Dimer of Pro-apoptotic BAX (I) -

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Basic information

Entry
Database: PDB / ID: 4s0o
TitleCrystal Structure of the Autoinhibited Dimer of Pro-apoptotic BAX (I)
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / BCL-2 FAMILY PROTEIN / APOPTOSIS REGULATOR / AUTOINHIBITED DIMER
Function / homology
Function and homology information


release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process ...release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process / Release of apoptotic factors from the mitochondria / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / endoplasmic reticulum calcium ion homeostasis / mitochondrial fusion / apoptotic mitochondrial changes / execution phase of apoptosis / Bcl-2 family protein complex / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of IRE1-mediated unfolded protein response / pore complex / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / cellular response to unfolded protein / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein binding / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / regulation of mitochondrial membrane potential / Hsp70 protein binding / apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to virus / positive regulation of protein-containing complex assembly / response to toxic substance / positive regulation of neuron apoptotic process / nuclear envelope / channel activity / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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: 1.9 Å
AuthorsPriyadarshi, A. / Gavathiotis, E.
CitationJournal: Mol.Cell / Year: 2016
Title: An Autoinhibited Dimeric Form of BAX Regulates the BAX Activation Pathway.
Authors: Garner, T.P. / Reyna, D.E. / Priyadarshi, A. / Chen, H.C. / Li, S. / Wu, Y. / Ganesan, Y.T. / Malashkevich, V.N. / Almo, S.S. / Cheng, E.H. / Gavathiotis, E.
History
DepositionJan 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)42,3292
Polymers42,3292
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-8 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.657, 40.276, 65.303
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21164.291 Da / Num. of mol.: 2 / Mutation: P168G
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.6 M AMMONIUM SULFATE, 0.1 M BIS-TRIS , PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24766 / Num. obs: 24766 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.07 / Net I/σ(I): 21.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.23 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F16

1f16


Resolution: 1.9→19.15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.35 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1315 5 %RANDOM
Rwork0.209 ---
obs0.212 24766 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.03 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 0 124 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9593807
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07523.898118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94315492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0351518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212074
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3421.51738
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21922787
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.19731076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8774.51020
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 83 -
Rwork0.267 1818 -
obs--99.95 %
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)
12.2922-0.00170.71460.74310.37540.9852-0.1057-0.1624-0.0680.10710.0899-0.11960.0313-0.00930.01580.07350.0323-0.0190.0249-0.01160.03854.8697-0.470813.2349
22.26920.0235-0.90870.84010.19830.9898-0.08890.13840.0593-0.10180.089-0.1309-0.0191-0.0019-0.00010.0672-0.0305-0.00840.0226-0.00210.034836.62180.1219.4609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 192
2X-RAY DIFFRACTION2B13 - 192

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