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

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Basic information

Entry
Database: PDB / ID: 4zig
TitleCrystal Structure of core/latch dimer of Bax in complex with BidBH3mini
Components
  • Apoptosis regulator BAX
  • BH3-interacting domain death agonist
KeywordsAPOPTOSIS / Bax / BH3 domain / Structural Genomics / The Walter and Eliza Hall Institute of Medical Research
Function / homology
Function and homology information


cysteine-type endopeptidase regulator activity involved in apoptotic process / 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 / mitochondrial outer membrane permeabilization / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process ...cysteine-type endopeptidase regulator activity involved in apoptotic process / 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 / mitochondrial outer membrane permeabilization / 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 / Activation and oligomerization of BAK protein / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / Activation, myristolyation of BID and translocation to mitochondria / 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 / 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 / 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 / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to mitochondrion / regulation of epithelial cell proliferation / establishment of protein localization to membrane / endoplasmic reticulum calcium ion homeostasis / death receptor binding / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / 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 / regulation of T cell proliferation / thymocyte apoptotic process / hepatocyte apoptotic process / pore complex / BH3 domain binding / germ cell development / mitochondrial ATP synthesis coupled electron transport / regulation of G1/S transition of mitotic cell cycle / 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 / Activation of BAD and translocation to mitochondria / ectopic germ cell programmed cell death / cellular response to unfolded protein / blood vessel remodeling / signal transduction in response to DNA damage / 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
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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. ...BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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
BH3-interacting domain death agonist / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator BAX
B: BH3-interacting domain death agonist


Theoretical massNumber of molelcules
Total (without water)20,8232
Polymers20,8232
Non-polymers00
Water63135
1
A: Apoptosis regulator BAX
B: BH3-interacting domain death agonist

A: Apoptosis regulator BAX
B: BH3-interacting domain death agonist


Theoretical massNumber of molelcules
Total (without water)41,6454
Polymers41,6454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_778-y+2,-x+2,-z+7/21
Buried area3880 Å2
ΔGint-32 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.120, 100.120, 37.410
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 BH3-interacting domain death agonist / p22 BID / BID


Mass: 2310.568 Da / Num. of mol.: 1 / Fragment: BH3 motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
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: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→19.96 Å / Num. obs: 10108 / % possible obs: 99.96 % / Redundancy: 7.8 % / Net I/σ(I): 15.18
Reflection shellResolution: 2.2→2.278 Å / Redundancy: 8 % / Rmerge(I) obs: 0.8454 / Mean I/σ(I) obs: 2.61 / % possible all: 100

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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: 2.2→19.959 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 506 5.01 %
Rwork0.1808 --
obs0.1832 10107 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 0 35 1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081411
X-RAY DIFFRACTIONf_angle_d0.9811908
X-RAY DIFFRACTIONf_dihedral_angle_d14.707534
X-RAY DIFFRACTIONf_chiral_restr0.038209
X-RAY DIFFRACTIONf_plane_restr0.004250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.42110.2471230.1982331X-RAY DIFFRACTION100
2.4211-2.77070.25971240.20582360X-RAY DIFFRACTION100
2.7707-3.48770.24981260.19952392X-RAY DIFFRACTION100
3.4877-19.960.20611330.1612518X-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)
12.23450.73270.40531.71490.25791.74330.08250.03260.01120.0328-0.00970.17360.0165-0.2004-0.00050.16950.00680.00170.24840.04130.2245124.000899.417879.3159
20.36560.47060.22070.49550.22910.111-0.0315-0.0448-0.0396-0.1537-0.00320.0704-0.07180.06830.00010.2725-0.00590.00940.21720.03240.250199.439567.98786.0486
30.26720.0112-0.07650.2217-0.03920.0547-0.14760.69950.2276-0.6324-0.10370.2158-0.03120.1033-0.01990.3436-0.0523-0.04230.43130.10720.3146126.065599.832864.6304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:128 )A10 - 128
2X-RAY DIFFRACTION2( CHAIN A AND RESID 129:166 )A129 - 166
3X-RAY DIFFRACTION3( CHAIN B AND RESID 78:98 )B78 - 98

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