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- PDB-4bd7: Bax domain swapped dimer induced by octylmaltoside -

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Basic information

Entry
Database: PDB / ID: 4bd7
TitleBax domain swapped dimer induced by octylmaltoside
ComponentsAPOPTOSIS REGULATOR BAX
KeywordsAPOPTOSIS / PROGRAMMED CELL DEATH
Function / homology
Function and homology information


positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / development of animal secondary sexual characteristics / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / regulation of mammary gland epithelial cell proliferation ...positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / development of animal secondary sexual characteristics / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / apoptotic process involved in mammary gland involution / apoptotic process involved in embryonic digit morphogenesis / B cell negative selection / BAK complex / retinal cell programmed cell death / glycosphingolipid metabolic process / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of apoptotic process involved in mammary gland involution / B cell apoptotic process / regulation of nitrogen utilization / endoplasmic reticulum calcium ion homeostasis / fertilization / epithelial cell apoptotic process / motor neuron apoptotic process / calcium ion transport into cytosol / positive regulation of epithelial cell apoptotic process / mitochondrial fusion / myeloid cell homeostasis / Bcl-2 family protein complex / execution phase of apoptosis / odontogenesis of dentin-containing tooth / thymocyte apoptotic process / B cell homeostasis / hypothalamus development / positive regulation of IRE1-mediated unfolded protein response / pore complex / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / vagina development / germ cell development / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / negative regulation of apoptotic signaling pathway / cellular response to unfolded protein / positive regulation of calcium ion transport into cytosol / Pyroptosis / response to axon injury / blood vessel remodeling / negative regulation of protein binding / ectopic germ cell programmed cell death / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / release of sequestered calcium ion into cytosol / positive regulation of intrinsic apoptotic signaling pathway / response to salt stress / supramolecular fiber organization / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / intrinsic apoptotic signaling pathway / Hsp70 protein binding / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitochondrial membrane potential / kidney development / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cerebral cortex development / cellular response to virus / neuron migration / intrinsic apoptotic signaling pathway in response to DNA damage / response to toxic substance / cellular response to UV / nuclear envelope / positive regulation of neuron apoptotic process / channel activity / retina development in camera-type eye / 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
PRASEODYMIUM ION / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 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 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)77,0487
Polymers76,7314
Non-polymers3173
Water27015
1
A: APOPTOSIS REGULATOR BAX
B: APOPTOSIS REGULATOR BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6835
Polymers38,3652
Non-polymers3173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-89.7 kcal/mol
Surface area14820 Å2
MethodPISA
2
C: APOPTOSIS REGULATOR BAX
D: APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)38,3652
Polymers38,3652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-84.2 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.237, 142.237, 86.775
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-1172-

CL

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6298, -0.2339, -0.7407), (-0.2342, -0.9664, 0.106), (-0.7406, 0.1067, -0.6634)91.18, 200.4607, 137.4371
2given(0.5711, -0.818, -0.0688), (-0.64, -0.3912, -0.6613), (0.5141, 0.4217, -0.7469)68.3878, 218.4172, 45.5994
3given(0.0167, -0.6676, 0.7444), (0.5467, 0.6294, 0.5522), (-0.8371, 0.3977, 0.3755)47.5565, -22.2568, 77.9535

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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.: 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


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.07 Å3/Da / Density % sol: 59.98 % / 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: 1.5498
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16061 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 73.61 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.87 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.801→41.026 Å / SU ML: 0.47 / σ(F): 1.97 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 806 5 %
Rwork0.2006 --
obs0.2042 16050 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.801→41.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 3 15 4227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094299
X-RAY DIFFRACTIONf_angle_d1.2565837
X-RAY DIFFRACTIONf_dihedral_angle_d15.611447
X-RAY DIFFRACTIONf_chiral_restr0.078668
X-RAY DIFFRACTIONf_plane_restr0.004732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.801-2.97650.41691280.3252523X-RAY DIFFRACTION99
2.9765-3.20620.31871270.25962573X-RAY DIFFRACTION100
3.2062-3.52870.27331520.19972494X-RAY DIFFRACTION100
3.5287-4.03890.25311380.18592547X-RAY DIFFRACTION100
4.0389-5.08710.26961350.17892563X-RAY DIFFRACTION100
5.0871-41.03030.25841260.19372544X-RAY DIFFRACTION100
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)
14.02631.54160.51654.16670.06663.73160.0608-0.1883-0.05130.1711-0.0280.4597-0.2680.02870.10090.3420.0205-0.0110.3691-0.00040.742953.6676119.493767.2819
21.3791-0.1890.13593.3529-0.43091.63730.3334-0.0153-0.09591.0554-0.2324-0.00240.5684-0.0621-0.1080.51570.0301-0.01510.43660.01590.289448.356588.892270.6918
32.6747-0.60960.58722.2062-0.5165.07630.3799-0.3820.25830.1243-0.2318-0.18960.4376-0.279-0.04350.51760.00160.02590.6495-0.03350.40949.085281.230767.4854
41.68150.43230.05682.6295-0.99671.3557-0.0130.03410.5835-0.35730.04550.85740.0926-0.1392-0.10280.36090.00330.05350.43170.05890.401747.7693107.035564.3037
51.43022.0485-0.43163.24480.47984.54560.0182-0.6468-1.333-0.17680.00740.39460.76480.0495-0.01141.23270.2036-0.33950.6119-0.09971.160960.527158.542857.8681
62.0065-0.7665-0.55670.75971.45913.47930.3260.5071-0.8608-0.5442-0.4430.67031.83081.28330.11931.77480.7433-0.31340.9252-0.30661.766968.210450.782652.5597
72.59473.25872.93027.94941.25834.95550.06831.8804-0.8417-2.3509-0.5193-0.23361.19271.0283-0.01921.52130.490.23261.23070.20211.102474.786464.795441.803
86.99161.28111.51382.57-0.00988.23820.40721.53210.1314-0.9689-0.07120.4104-0.830.4710.58291.19540.8022-0.29231.3804-0.35020.953764.174369.311743.2859
93.8807-0.11342.43923.36511.82934.2608-0.09260.9745-0.2527-0.21240.0054-0.6962-0.15451.40170.26070.50030.1425-0.04090.74630.19450.494582.084476.584466.3457
102.1734-0.53151.82594.86231.88333.62821.09980.2559-0.05571.4858-0.681-0.36780.82270.78460.04281.03590.0759-0.12490.94260.21060.792291.738175.900377.6027
115.41991.35431.00227.11691.69513.5276-0.5847-0.59920.19820.1402-0.54671.1680.22160.14390.48930.9373-0.0059-0.08290.82380.23361.213678.219787.262780.0032
123.48120.81862.20614.43131.66643.52450.5763-0.0336-0.3401-0.0424-0.66930.09430.3954-0.40720.10290.56780.10580.00410.69930.09570.46870.351872.535364.7666
131.77852.5725-2.90075.2067-3.86155.6149-0.61950.1748-1.0087-0.7136-0.1479-0.45311.24480.1017-0.40971.90760.4625-0.31590.8233-0.49751.865164.79350.773541.9261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 14 THROUGH 106 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 107 THROUGH 170 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 14 THROUGH 100 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 101 THROUGH 170 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 15 THROUGH 34 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 35 THROUGH 72 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 73 THROUGH 88 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 89 THROUGH 100 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 101 THROUGH 170 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 16 THROUGH 71 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 72 THROUGH 100 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 101 THROUGH 160 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 161 THROUGH 170 )

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