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- PDB-4s0p: Crystal Structure of the Autoinhibited Dimer of Pro-apoptotic BAX (II) -

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Basic information

Entry
Database: PDB / ID: 4s0p
TitleCrystal Structure of the Autoinhibited Dimer of Pro-apoptotic BAX (II)
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 / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / cellular response to unfolded protein / Pyroptosis / negative regulation of protein binding / extrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / apoptotic signaling pathway / regulation of mitochondrial membrane potential / Hsp70 protein binding / 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: 3.252 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 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references / Derived calculations
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Sep 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)42,6092
Polymers42,6092
Non-polymers00
Water00
1
A: Apoptosis regulator BAX

A: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)42,6092
Polymers42,6092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area17120 Å2
MethodPISA
2
B: Apoptosis regulator BAX

B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)42,6092
Polymers42,6092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
MethodPISA
Unit cell
Length a, b, c (Å)40.587, 65.010, 65.590
Angle α, β, γ (deg.)90.00, 89.87, 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: 21304.498 Da / Num. of mol.: 2 / Mutation: G67R
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

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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: 2.03 Å3/Da / Density % sol: 39.43 %
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: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 5419 / Num. obs: 4866 / % possible obs: 89.8 % / Observed criterion σ(F): -3
Reflection shellResolution: 3.25→3.31 Å / % possible all: 78.3

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0072refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F16

1f16


Resolution: 3.252→46.173 Å / SU ML: 0.38 / σ(F): 1.55 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 256 5.27 %
Rwork0.2106 --
obs0.2141 4859 88.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.252→46.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 0 0 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112812
X-RAY DIFFRACTIONf_angle_d1.2653806
X-RAY DIFFRACTIONf_dihedral_angle_d19.5121022
X-RAY DIFFRACTIONf_chiral_restr0.052434
X-RAY DIFFRACTIONf_plane_restr0.007476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2516-4.09630.2748900.20562188X-RAY DIFFRACTION84
4.0963-46.17730.26721660.21352415X-RAY DIFFRACTION94

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