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- PDB-4bd2: Bax domain swapped dimer in complex with BidBH3 -

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Basic information

Entry
Database: PDB / ID: 4bd2
TitleBax domain swapped dimer in complex with BidBH3
Components
  • APOPTOSIS REGULATOR BAX
  • BH3-INTERACTING DOMAIN DEATH AGONIST
KeywordsAPOPTOSIS / PROGRAMMED CELL DEATH / BCL-2 FAMILY.
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 / Resolution: 2.206 Å
AuthorsCzabotar, P.E. / Westphal, D. / Adams, J.M. / Colman, P.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Bax Crystal Structures Reveal How Bh3 Domains Activate Bax and Nucleate its Oligomerization to Induce Apoptosis.
Authors: Czabotar, P.E. / Westphal, D. / Dewson, G. / Ma, S. / Hockings, C. / Fairlie, W.D. / Lee, E.F. / Yao, S. / Robin, A.Y. / Smith, B.J. / Huang, D.C. / Kluck, R.M. / Adams, J.M. / Colman, P.M.
History
DepositionOct 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)22,8762
Polymers22,8762
Non-polymers00
Water1,29772
1
A: APOPTOSIS REGULATOR BAX
C: BH3-INTERACTING DOMAIN DEATH AGONIST

A: APOPTOSIS REGULATOR BAX
C: BH3-INTERACTING DOMAIN DEATH AGONIST


Theoretical massNumber of molelcules
Total (without water)45,7524
Polymers45,7524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_557-y,-x,-z+5/21
Buried area11300 Å2
ΔGint-124.8 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.962, 101.962, 37.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-2003-

HOH

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Components

#1: Protein APOPTOSIS REGULATOR BAX / BAX / BCL-2-LIKE PROTEIN 4 / BCL2-L-4


Mass: 19182.711 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-171 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q07812
#2: Protein/peptide BH3-INTERACTING DOMAIN DEATH AGONIST / BIDBH3 / P22 BID / BID / BH3-INTERACTING DOMAIN DEATH AGONIST P P15 BID / BH3-INTERACTING DOMAIN ...BIDBH3 / P22 BID / BID / BH3-INTERACTING DOMAIN DEATH AGONIST P P15 BID / BH3-INTERACTING DOMAIN DEATH AGONIST P13 / P13 BID / BH3-INTERACTING DOMAIN DEATH AGONIST P11 / P11 BID


Mass: 3693.111 Da / Num. of mol.: 1 / Fragment: RESIDUES 76-109 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P55957
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.13 Å3/Da / Density % sol: 42.3 % / Description: NONE
Crystal growDetails: 1.4 M SODIUM CITRATE, 0.1 M SODIUM CACODYLATE PH 5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADXV / Detector: CCD / Date: Dec 5, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.21→51 Å / Num. obs: 10428 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 34.53 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 9.66
Reflection shellResolution: 2.21→2.43 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.02 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BAX DOMAIN SWAPPED DIMER INDUCED BY OCTYLMALTOSIDE

Resolution: 2.206→50.981 Å / SU ML: 0.32 / σ(F): 2 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 522 5 %
Rwork0.1763 --
obs0.179 10428 99.78 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.64 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 41.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.7605 Å20 Å20 Å2
2--0.7605 Å20 Å2
3----1.521 Å2
Refinement stepCycle: LAST / Resolution: 2.206→50.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 0 72 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081407
X-RAY DIFFRACTIONf_angle_d0.9731894
X-RAY DIFFRACTIONf_dihedral_angle_d14.018524
X-RAY DIFFRACTIONf_chiral_restr0.064208
X-RAY DIFFRACTIONf_plane_restr0.004245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.206-2.4280.33131260.24372388X-RAY DIFFRACTION99
2.428-2.77930.27241280.20232438X-RAY DIFFRACTION100
2.7793-3.50150.25791300.17882474X-RAY DIFFRACTION100
3.5015-50.99460.17711380.15292606X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.9614 Å / Origin y: -8.1719 Å / Origin z: 41.7997 Å
111213212223313233
T0.1821 Å2-0.0289 Å20.0004 Å2-0.2134 Å20.0608 Å2--0.17 Å2
L0.9404 °20.7919 °2-0.2135 °2-0.902 °2-0.0499 °2---0.0819 °2
S-0.0219 Å °0.0928 Å °0.1052 Å °-0.0677 Å °0.0649 Å °0.0988 Å °0.0408 Å °-0.0095 Å °0.0094 Å °
Refinement TLS groupSelection details: ALL

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