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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 / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / mitochondrial outer membrane permeabilization / 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 / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / mitochondrial outer membrane permeabilization / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / spermatid differentiation / Activation and oligomerization of BAK protein / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / positive regulation of B cell apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / glycosphingolipid metabolic process / retinal cell programmed cell death / B cell negative selection / BAK complex / Activation, myristolyation of BID and translocation to mitochondria / 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 / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / regulation of nitrogen utilization / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / B cell apoptotic process / regulation of epithelial cell proliferation / endoplasmic reticulum calcium ion homeostasis / establishment of protein localization to membrane / positive regulation of epithelial cell apoptotic process / fertilization / death receptor binding / calcium ion transport into cytosol / positive regulation of extrinsic apoptotic signaling pathway / epithelial cell apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / positive regulation of mitochondrial membrane potential / myeloid cell homeostasis / motor neuron apoptotic process / protein targeting to mitochondrion / execution phase of apoptosis / thymocyte apoptotic process / hepatocyte apoptotic process / hypothalamus development / pore complex / positive regulation of IRE1-mediated unfolded protein response / mitochondrial ATP synthesis coupled electron transport / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / apoptotic mitochondrial changes / BH3 domain binding / vagina development / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of T cell proliferation / B cell homeostasis / positive regulation of calcium ion transport into cytosol / regulation of G1/S transition of mitotic cell cycle / negative regulation of apoptotic signaling pathway / signal transduction in response to DNA damage / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / Activation of BAD and translocation to mitochondria / ectopic germ cell programmed cell death / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of protein binding / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / extrinsic apoptotic signaling pathway / response to salt stress / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / Hsp70 protein binding / homeostasis of number of cells within a tissue / intrinsic apoptotic signaling pathway
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-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
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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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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