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- PDB-8spe: Crystal structure of Bax core domain BH3-groove dimer - tetrameri... -

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Basic information

Entry
Database: PDB / ID: 8spe
TitleCrystal structure of Bax core domain BH3-groove dimer - tetrameric fraction P31
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / BAX / BCL2
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 / B cell negative selection / BAK complex / positive regulation of reproductive process / positive regulation of mitochondrial membrane permeability 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 / B cell negative selection / BAK complex / positive regulation of reproductive process / positive regulation of mitochondrial membrane permeability involved in apoptotic 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 / apoptotic process involved in blood vessel morphogenesis / NTRK3 as a dependence receptor / negative regulation of endoplasmic reticulum calcium ion concentration / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / glycosphingolipid metabolic process / Release of apoptotic factors from the mitochondria / B cell homeostatic proliferation / apoptotic process involved in embryonic digit morphogenesis / retinal cell programmed cell death / post-embryonic camera-type eye morphogenesis / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / mitochondrial fragmentation involved in apoptotic process / establishment or maintenance of transmembrane electrochemical gradient / mitochondrial permeability transition pore complex / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / B cell apoptotic process / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / fertilization / calcium ion transport into cytosol / myeloid cell homeostasis / Bcl-2 family protein complex / mitochondrial fusion / positive regulation of epithelial cell apoptotic process / motor neuron apoptotic process / BH domain binding / epithelial cell apoptotic process / thymocyte apoptotic process / execution phase of apoptosis / positive regulation of calcium ion transport into cytosol / hypothalamus development / pore complex / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / negative regulation of peptidyl-serine phosphorylation / B cell homeostasis / vagina development / BH3 domain binding / germ cell development / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / apoptotic mitochondrial changes / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / ectopic germ cell programmed cell death / Pyroptosis / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / cellular response to unfolded protein / response to axon injury / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / negative regulation of fibroblast proliferation / supramolecular fiber organization / homeostasis of number of cells within a tissue / response to salt stress / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway / Hsp70 protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / kidney development / regulation of mitochondrial membrane potential / apoptotic signaling pathway / negative regulation of protein binding / response to gamma radiation / positive regulation of protein-containing complex assembly / neuron migration / cellular response to virus / cerebral cortex development / response to toxic substance / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / cellular response to UV / channel activity
Similarity search - Function
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, 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 / BCL2-like apoptosis inhibitors family profile. / Apoptosis regulator proteins, Bcl-2 family / Bcl-2-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiller, M.S. / Cowan, A.D. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Febs J. / Year: 2024
Title: Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids.
Authors: Miller, M.S. / Cowan, A.D. / Brouwer, J.M. / Smyth, S.T. / Peng, L. / Wardak, A.Z. / Uren, R.T. / Luo, C. / Roy, M.J. / Shah, S. / Tan, Z. / Reid, G.E. / Colman, P.M. / Czabotar, P.E.
History
DepositionMay 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX
Q: Apoptosis regulator BAX
R: Apoptosis regulator BAX
S: Apoptosis regulator BAX
T: Apoptosis regulator BAX
G: Apoptosis regulator BAX
H: Apoptosis regulator BAX
U: Apoptosis regulator BAX
V: Apoptosis regulator BAX
E: Apoptosis regulator BAX
F: Apoptosis regulator BAX
I: Apoptosis regulator BAX
J: Apoptosis regulator BAX
K: Apoptosis regulator BAX
L: Apoptosis regulator BAX
M: Apoptosis regulator BAX
N: Apoptosis regulator BAX
O: Apoptosis regulator BAX
P: Apoptosis regulator BAX
W: Apoptosis regulator BAX
X: Apoptosis regulator BAX
Y: Apoptosis regulator BAX
Z: Apoptosis regulator BAX
a: Apoptosis regulator BAX
b: Apoptosis regulator BAX
c: Apoptosis regulator BAX
d: Apoptosis regulator BAX
e: Apoptosis regulator BAX
f: Apoptosis regulator BAX
g: Apoptosis regulator BAX
h: Apoptosis regulator BAX
i: Apoptosis regulator BAX
j: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,06752
Polymers323,00036
Non-polymers1,06716
Water68538
1
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,27510
Polymers35,8894
Non-polymers3866
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: Apoptosis regulator BAX
R: Apoptosis regulator BAX
S: Apoptosis regulator BAX
T: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)35,8894
Polymers35,8894
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Apoptosis regulator BAX
H: Apoptosis regulator BAX
U: Apoptosis regulator BAX
V: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)35,8894
Polymers35,8894
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Apoptosis regulator BAX
F: Apoptosis regulator BAX
I: Apoptosis regulator BAX
J: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,31210
Polymers35,8894
Non-polymers4236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: Apoptosis regulator BAX
L: Apoptosis regulator BAX
M: Apoptosis regulator BAX
N: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0166
Polymers35,8894
Non-polymers1272
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
O: Apoptosis regulator BAX
P: Apoptosis regulator BAX
W: Apoptosis regulator BAX
X: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)35,8894
Polymers35,8894
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
Y: Apoptosis regulator BAX
Z: Apoptosis regulator BAX
a: Apoptosis regulator BAX
b: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)35,8894
Polymers35,8894
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
c: Apoptosis regulator BAX
d: Apoptosis regulator BAX
e: Apoptosis regulator BAX
f: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9545
Polymers35,8894
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
g: Apoptosis regulator BAX
h: Apoptosis regulator BAX
i: Apoptosis regulator BAX
j: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9545
Polymers35,8894
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.355, 141.355, 110.191
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein ...
Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 8972.228 Da / Num. of mol.: 36
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M NaMES pH 5.6, 27% PEG MME550, 0.01 M Zinc sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→46.27 Å / Num. obs: 108680 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.051 / Rrim(I) all: 0.122 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.34 Å / % possible obs: 96.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 1.788 / Num. measured all: 28318 / Num. unique obs: 5174 / CC1/2: 0.464 / Rpim(I) all: 0.829 / Rrim(I) all: 1.973 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.43 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 1992 1.83 %
Rwork0.2289 --
obs0.2294 108680 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18907 0 40 38 18985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01219242
X-RAY DIFFRACTIONf_angle_d0.67625863
X-RAY DIFFRACTIONf_dihedral_angle_d17.1696807
X-RAY DIFFRACTIONf_chiral_restr0.0342913
X-RAY DIFFRACTIONf_plane_restr0.0063299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.33741400.32067315X-RAY DIFFRACTION95
2.36-2.420.34361440.30557680X-RAY DIFFRACTION100
2.42-2.490.33251400.28387606X-RAY DIFFRACTION100
2.49-2.580.29861420.27897617X-RAY DIFFRACTION100
2.58-2.670.36941420.28077693X-RAY DIFFRACTION100
2.67-2.770.34261420.27487649X-RAY DIFFRACTION100
2.77-2.90.30951450.26167616X-RAY DIFFRACTION100
2.9-3.050.28011440.27917644X-RAY DIFFRACTION100
3.05-3.240.26711440.25937639X-RAY DIFFRACTION100
3.24-3.490.26961380.2457669X-RAY DIFFRACTION100
3.49-3.840.23981400.20887628X-RAY DIFFRACTION100
3.85-4.40.24571440.20167675X-RAY DIFFRACTION100
4.4-5.540.23351440.19877614X-RAY DIFFRACTION100
5.54-35.430.21430.19677643X-RAY DIFFRACTION100

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