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- PDB-4bdu: Bax BH3-in-Groove dimer (GFP) -

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Basic information

Entry
Database: PDB / ID: 4bdu
TitleBax BH3-in-Groove dimer (GFP)
ComponentsGREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
KeywordsAPOPTOSIS / PROGRAMMED CELL DEATH / BCL-2 FAMILY / CHIMERA
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 / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / 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 / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / 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 / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of apoptotic signaling pathway / 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 / ectopic germ cell programmed cell death / cellular response to unfolded protein / blood vessel remodeling / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / bioluminescence / 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 / generation of precursor metabolites and energy / kidney development / response to gamma radiation / apoptotic signaling pathway / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cerebral cortex development / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to UV
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 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Green fluorescent protein / Apoptosis regulator BAX
Similarity search - Component
Biological speciesAEQUOREA VICTORIA (jellyfish)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å
AuthorsCzabotar, P.E. / 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 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
B: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
C: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
D: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)139,6334
Polymers139,6334
Non-polymers00
Water1,51384
1
A: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
B: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX

A: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
B: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)139,6334
Polymers139,6334
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area11450 Å2
ΔGint-82 kcal/mol
Surface area55010 Å2
MethodPISA
2
C: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
D: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX

C: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX
D: GREEN FLUORESCENT PROTEIN, APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)139,6334
Polymers139,6334
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area11450 Å2
ΔGint-81 kcal/mol
Surface area55010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.314, 112.314, 293.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:64 OR RESSEQ 68:230)
211CHAIN B AND (RESSEQ 2:64 OR RESSEQ 68:230)
311CHAIN C AND (RESSEQ 2:64 OR RESSEQ 68:230)
411CHAIN D AND (RESSEQ 2:64 OR RESSEQ 68:230)
112CHAIN A AND (RESSEQ 1054:1122)
212CHAIN B AND (RESSEQ 1054:1122)
312CHAIN C AND (RESSEQ 1054:1122)
412CHAIN D AND (RESSEQ 1054:1122)

NCS ensembles :
ID
1
2

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Components

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


Mass: 34908.332 Da / Num. of mol.: 4 / Fragment: BAX RESIDUES 53-128 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish), (gene. exp.) HOMO SAPIENS (human)
Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P42212, UniProt: Q07812
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF GFP IS AS DESCRIBED IN SUZUKI ET AL. (2010) ACTA CRYS D 66, 1059, BEARING THE EXTRA ...THE SEQUENCE OF GFP IS AS DESCRIBED IN SUZUKI ET AL. (2010) ACTA CRYS D 66, 1059, BEARING THE EXTRA MUTATION, A206N BAX TRUNCATED TO LEAVE ALPHA2 TO ALPHA5, MUTATIONS S62C, S126C. GFP AND BAX CRYSTALLIZED AS A SINGLE FUSION PROTEIN. 1000 HAS BEEN ADDED TO THE SEQUENCE NUMBERING OF BAX TO PRESERVE UNP NUMBERING.

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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: 3.75 Å3/Da / Density % sol: 67.22 % / Description: NONE
Crystal growDetails: 10% PEG3350, 20% MPD, 0.5% CHAPS, 0.1 M TRIS PH 8.0

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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: May 25, 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: 3→19.9 Å / Num. obs: 41413 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 20.7 % / Biso Wilson estimate: 82.07 Å2 / Rmerge(I) obs: 0.1731 / Net I/σ(I): 17.74
Reflection shellResolution: 3→3.1 Å / Redundancy: 17.5 % / Rmerge(I) obs: 1.731 / Mean I/σ(I) obs: 2.26 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.998→19.959 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 31.34 / Stereochemistry target values: ML
Details: CONSTRUCT USED FOR CRYSTALLISATION CONSISTED OF GFP FUSED TO BAX AS DESCRIBED IN SUZUKI ET AL. (2010) ACTA CRYS D 66, 1059.
RfactorNum. reflection% reflection
Rfree0.246 2071 5 %
Rwork0.2149 --
obs0.2165 41413 99.38 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.524 Å2 / ksol: 0.263 e/Å3
Displacement parametersBiso mean: 120.51 Å2
Baniso -1Baniso -2Baniso -3
1-2.8299 Å20 Å20 Å2
2--2.8299 Å20 Å2
3----5.6597 Å2
Refinement stepCycle: LAST / Resolution: 2.998→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9464 0 0 84 9548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099676
X-RAY DIFFRACTIONf_angle_d1.3913072
X-RAY DIFFRACTIONf_dihedral_angle_d15.0873544
X-RAY DIFFRACTIONf_chiral_restr0.1121404
X-RAY DIFFRACTIONf_plane_restr0.0041696
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1799X-RAY DIFFRACTIONPOSITIONAL
12B1799X-RAY DIFFRACTIONPOSITIONAL0.223
13C1799X-RAY DIFFRACTIONPOSITIONAL0.225
14D1799X-RAY DIFFRACTIONPOSITIONAL0.111
21A548X-RAY DIFFRACTIONPOSITIONAL
22B548X-RAY DIFFRACTIONPOSITIONAL0.021
23C548X-RAY DIFFRACTIONPOSITIONAL0.022
24D548X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9984-3.06790.36561070.35472478X-RAY DIFFRACTION94
3.0679-3.14440.32422100.30992568X-RAY DIFFRACTION100
3.1444-3.2290.36851090.27632657X-RAY DIFFRACTION100
3.229-3.32360.33061080.27312646X-RAY DIFFRACTION100
3.3236-3.43040.32251030.24732675X-RAY DIFFRACTION100
3.4304-3.55230.28542090.24452569X-RAY DIFFRACTION100
3.5523-3.69370.36421060.23342668X-RAY DIFFRACTION100
3.6937-3.86070.26521020.23142688X-RAY DIFFRACTION100
3.8607-4.06260.2692110.20972552X-RAY DIFFRACTION100
4.0626-4.31470.20981050.19192667X-RAY DIFFRACTION100
4.3147-4.6440.18421010.16962675X-RAY DIFFRACTION100
4.644-5.10430.19562050.16542587X-RAY DIFFRACTION100
5.1043-5.82670.27961010.19962661X-RAY DIFFRACTION100
5.8267-7.28130.2311020.22662681X-RAY DIFFRACTION100
7.2813-19.95920.20391920.19982570X-RAY DIFFRACTION98
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)
10.0498-0.00090.0190.03090.00990.0261-0.02410.1045-0.0535-0.0223-0.0383-0.0212-0.02380.0694-0.03561.2765-0.41460.16660.2384-0.07820.312714.5202102.1189103.9046
20.0389-0.01850.00450.0236-0.00480.0382-0.047-0.11960.08810.0122-0.0234-0.00440.0850.2035-0.06960.69420.6282-0.09130.7536-0.00310.350214.501392.424630.2147
30.01870.00670.01830.05240.00790.0409-0.03150.0364-0.0381-0.110.050.0388-0.25350.03390.00140.97750.37010.03710.06060.04060.644531.130863.6067135.2657
40.06240.0185-0.02260.0461-0.0160.01490.04540.02130.01220.0967-0.05440.0103-0.10390.0877-0.0227-0.16560.4455-0.03691.1744-0.17240.659139.552458.788661.5724
5-0.0018-0.0010.00150.00430.00420.00340.05850.08180.05670.00570.11310.0990.01540.1163-01.18970.192-0.02361.04810.09330.747614.387397.016767.0126
60.0077-0.0043-0.00950.00190.0020.00670.1256-0.0392-0.10490.04320.04230.0062-0.10350.04701.02410.2132-0.04030.91440.09420.698235.042861.225398.5901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:230
2X-RAY DIFFRACTION2CHAIN B AND RESID 1:230
3X-RAY DIFFRACTION3CHAIN C AND RESID 1:230
4X-RAY DIFFRACTION4CHAIN D AND RESID 1:230
5X-RAY DIFFRACTION5CHAIN A OR CHAIN B AND RESID 1053:1125
6X-RAY DIFFRACTION6CHAIN C OR CHAIN D AND RESID 1053:1125

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