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

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Basic information

Entry
Database: PDB / ID: 4zih
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
Function / homology
Function and homology information


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 / BIM-BCL-xl complex / BIM-BCL-2 complex / positive regulation of motor neuron 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 / BIM-BCL-xl complex / BIM-BCL-2 complex / positive regulation of motor neuron apoptotic process / 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 / NTRK3 as a dependence receptor / Sertoli cell proliferation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / glycosphingolipid metabolic process / B cell homeostatic proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / Activation of BIM and translocation to mitochondria / mitochondrial fragmentation involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / apoptotic process involved in blood vessel morphogenesis / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / developmental pigmentation / 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 / 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 / B cell apoptotic process / regulation of nitrogen utilization / mammary gland development / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / endoplasmic reticulum calcium ion homeostasis / positive regulation of epithelial cell apoptotic process / fertilization / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / epithelial cell apoptotic process / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / myeloid cell homeostasis / execution phase of apoptosis / apoptotic mitochondrial changes / hypothalamus development / NRAGE signals death through JNK / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / thymocyte apoptotic process / positive regulation of calcium ion transport into cytosol / pore complex / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / vagina development / odontogenesis of dentin-containing tooth / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / BH3 domain binding / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of mitochondrial membrane potential / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / Pyroptosis / cellular response to unfolded protein / ectopic germ cell programmed cell death / negative regulation of fibroblast proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / supramolecular fiber organization / positive regulation of intrinsic apoptotic signaling pathway / spleen development / extrinsic apoptotic signaling pathway / positive regulation of cell cycle / homeostasis of number of cells within a tissue / release of sequestered calcium ion into cytosol / response to salt stress
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, 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-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
Bcl-2-like protein 11 / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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)20,8572
Polymers20,8572
Non-polymers00
Water25214
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)41,7134
Polymers41,7134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9550 Å2
ΔGint-110 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.730, 95.730, 37.100
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: 18364.822 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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
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 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→19.68 Å / Num. obs: 6334 / % possible obs: 99.98 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.08496 / Net I/σ(I): 18.46
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 2.09 / % possible all: 99.84

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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: 2.5→19.68 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 317 5.01 %
Rwork0.1865 --
obs0.189 6333 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 0 14 1246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111269
X-RAY DIFFRACTIONf_angle_d1.6451715
X-RAY DIFFRACTIONf_dihedral_angle_d13.169458
X-RAY DIFFRACTIONf_chiral_restr0.076190
X-RAY DIFFRACTIONf_plane_restr0.012221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-3.14780.31161550.23292935X-RAY DIFFRACTION100
3.1478-19.68210.21021620.17313081X-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)
15.0362-0.52811.00343.95410.60833.9281-0.0524-0.1277-0.14930.31640.0726-0.5623-0.29910.4308-0.03370.3431-0.0477-0.01090.3556-0.01950.414124.9650.21223.611
23.2538-1.70121.81023.3918-0.39653.0904-0.0430.07380.3844-0.27-0.0679-0.09640.03170.12630.02980.3215-0.03580.0050.36850.03010.372950.21817.26616.759
33.9045-0.96450.06235.3981-1.22673.39010.3458-1.0627-0.05211.18290.0339-0.3773-0.0663-0.1659-0.02950.6356-0.0227-0.16960.6343-0.11810.423224.42352.33436.89
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 129:164 )A129 - 164
3X-RAY DIFFRACTION3( CHAIN B AND RESID 144:159 )B144 - 159

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