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- PDB-4zii: Crystal Structure of core/latch dimer of BaxI66A in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4zii
TitleCrystal Structure of core/latch dimer of BaxI66A in complex with BidBH3
Components
  • Apoptosis regulator BAX
  • BH3-interacting domain death agonist
KeywordsAPOPTOSIS / Bax / BH3 domain / Structural Genomics
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 / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / mitochondrial fragmentation involved in apoptotic process / 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 / 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 / endoplasmic reticulum calcium ion homeostasis / establishment of protein localization to membrane / death receptor binding / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of epithelial cell apoptotic process / positive regulation of mitochondrial membrane potential / calcium ion transport into cytosol / channel activity / motor neuron apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / hypothalamus development / regulation of T cell proliferation / hepatocyte apoptotic process / pore complex / thymocyte apoptotic process / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / regulation of G1/S transition of mitotic cell cycle / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / mitochondrial ATP synthesis coupled electron transport / vagina development / negative regulation of mitochondrial membrane potential / 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 / cellular response to unfolded protein / ectopic germ cell programmed cell death / blood vessel remodeling / signal transduction in response to DNA damage / Pyroptosis / supramolecular fiber organization / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / release of sequestered calcium ion into cytosol / ovarian follicle development / 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 / molecular replacement / Resolution: 2.191 Å
AuthorsCzabotar, P.E. / Robin, A.Y. / Krishna Kumar, K. / Westphal, D. / Wardak, A.Z. / Thompson, G.V. / Dewson, G. / Colman, P.M.
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
C: BH3-interacting domain death agonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8277
Polymers22,5162
Non-polymers3105
Water95553
1
A: Apoptosis regulator BAX
C: BH3-interacting domain death agonist
hetero molecules

A: Apoptosis regulator BAX
C: BH3-interacting domain death agonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,65414
Polymers45,0334
Non-polymers62110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area13440 Å2
ΔGint-111 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.801, 103.801, 38.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 18823.373 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: 3693.111 Da / Num. of mol.: 1 / Fragment: BH3 motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
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: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.191→46.42 Å / Num. obs: 11053 / % possible obs: 98.87 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.1086 / Net I/σ(I): 17.29
Reflection shellResolution: 2.191→2.269 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.947 / Mean I/σ(I) obs: 1.63 / % possible all: 94.33

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4bd2


Resolution: 2.191→46.42 Å / FOM work R set: 0.7954 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1106 10.01 %
Rwork0.1751 9943 -
obs0.18 11049 98.85 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.95 Å2 / Biso mean: 59.92 Å2 / Biso min: 19.78 Å2
Refinement stepCycle: final / Resolution: 2.191→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 20 53 1445
Biso mean--85.7 54.75 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071409
X-RAY DIFFRACTIONf_angle_d1.0541887
X-RAY DIFFRACTIONf_chiral_restr0.072207
X-RAY DIFFRACTIONf_plane_restr0.004244
X-RAY DIFFRACTIONf_dihedral_angle_d16.135519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1912-2.29090.42341300.36241169129995
2.2909-2.41170.29371350.24281218135399
2.4117-2.56270.25741360.19291216135299
2.5627-2.76060.2531360.18851231136799
2.7606-3.03830.22351370.18112341371100
3.0383-3.47790.23271410.17811261140299
3.4779-4.38120.19421400.144912651405100
4.3812-46.43160.19771510.15841349150099
Refinement TLS params.Method: refined / Origin x: 20.0334 Å / Origin y: -9.5138 Å / Origin z: 4.6275 Å
111213212223313233
T0.26 Å2-0.0488 Å2-0.0024 Å2-0.34 Å20.108 Å2--0.2728 Å2
L1.2249 °21.1108 °2-0.3059 °2-1.1708 °2-0.0616 °2---0.2743 °2
S-0.0306 Å °0.2025 Å °0.2165 Å °-0.0213 Å °0.1085 Å °0.2342 Å °0.0661 Å °-0.0409 Å °0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or chain CA10 - 167
2X-RAY DIFFRACTION1chain A or chain CC76 - 99

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