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- PDB-4zif: Crystal Structure of core/latch dimer of Bax in complex with BimB... -

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Basic information

Entry
Database: PDB / ID: 4zif
TitleCrystal Structure of core/latch dimer of Bax in complex with BimBH3mini
Components
  • Apoptosis regulator BAX
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Bax / BH3 domain / Structural Genomics / The Walter and Eliza Hall Institute of Medical Research
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 / BIM-BCL-xl complex / BIM-BCL-2 complex ...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 / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / 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 / RUNX3 regulates BCL2L11 (BIM) transcription / 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 / developmental pigmentation / BAK complex / Activation of BIM and translocation to mitochondria / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / positive regulation of fibroblast apoptotic process / 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 / ear development / tube formation / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / meiosis I / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / positive regulation of T cell apoptotic process / regulation of organ growth / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / cellular response to glucocorticoid stimulus / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / positive regulation of calcium ion transport into cytosol / hypothalamus development / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / pore complex / T cell homeostasis / BH3 domain binding / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / germ cell development / 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 / endomembrane system / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / positive regulation of cell cycle / 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 / ovarian follicle development / extrinsic apoptotic signaling pathway
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
Bcl-2-like protein 11 / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.401 Å
AuthorsRobin, A.Y. / Krishna Kumar, K. / Westphal, D. / Wardak, A.Z. / Thompson, G.V. / Dewson, G. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Projects Grant 1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)Projects Grant 1059331 Australia
National Health and Medical Research Council (NHMRC, Australia)Projects Grant 1023055 Australia
National Health and Medical Research Council (NHMRC, Australia)Program Grant 1016701 Australia
CitationJournal: Cell Death Dis / Year: 2015
Title: Crystal structure of Bax bound to the BH3 peptide of Bim identifies important contacts for interaction.
Authors: Robin, A.Y. / Krishna Kumar, K. / Westphal, D. / Wardak, A.Z. / Thompson, G.V. / Dewson, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator BAX
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)21,0042
Polymers21,0042
Non-polymers00
Water28816
1
A: Apoptosis regulator BAX
B: Bcl-2-like protein 11

A: Apoptosis regulator BAX
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)42,0084
Polymers42,0084
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area9690 Å2
ΔGint-110 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.140, 96.140, 37.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18511.996 Da / Num. of mol.: 1 / Mutation: C62S C126S
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: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 2491.800 Da / Num. of mol.: 1 / Fragment: BH3 motif, unp residues 141-160 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Tri-sodium citrate, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.401→19.77 Å / Num. obs: 7219 / % possible obs: 99.92 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.05781 / Net I/σ(I): 22.48
Reflection shellResolution: 2.401→2.486 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.7918 / Mean I/σ(I) obs: 2.61 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BD2

4bd2


Resolution: 2.401→19.766 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 361 5 %
Rwork0.195 --
obs0.198 7219 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→19.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 0 16 1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121291
X-RAY DIFFRACTIONf_angle_d1.5851746
X-RAY DIFFRACTIONf_dihedral_angle_d13.706468
X-RAY DIFFRACTIONf_chiral_restr0.082192
X-RAY DIFFRACTIONf_plane_restr0.009226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4005-2.74710.3581170.24962226X-RAY DIFFRACTION100
2.7471-3.4580.28411190.22222251X-RAY DIFFRACTION100
3.458-19.76660.22851250.17612381X-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)
17.5898-0.1895-0.30475.5091-0.66053.2120.2041-0.49710.36210.2654-0.03050.3856-0.0554-0.4262-0.07310.4265-0.07020.04970.41380.02810.375570.79246.15441.892
29.1648-4.146-2.14446.94980.52395.23440.01110.0292-0.0968-0.2166-0.19070.1175-0.1865-0.05990.19870.3999-0.05970.02770.3473-0.08740.339845.10578.71936.273
33.23373.26811.25939.35481.51062.22030.239-1.2216-0.26971.5612-0.33580.47120.2694-0.1403-0.16160.8854-0.13050.10780.94390.14730.525671.84443.78254.855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:128 )A11 - 128
2X-RAY DIFFRACTION2( CHAIN A AND RESID 129:166 )A129 - 166
3X-RAY DIFFRACTION3( CHAIN B AND RESID 144:159 )B144 - 159

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