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- PDB-6xy6: Structural insight into sheep-pox virus mediated inhibition of ap... -

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Basic information

Entry
Database: PDB / ID: 6xy6
TitleStructural insight into sheep-pox virus mediated inhibition of apoptosis
Components
  • (anti-apoptotic membrane protein) x 2
  • Apoptosis regulator BAX
KeywordsAPOPTOSIS / Pox virus / Bcl-2
Function / homology
Function and homology information


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 / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...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 / 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 / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / : / 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 / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / 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 / Transcriptional regulation by RUNX2 / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / calcium ion transport into cytosol / channel activity / motor neuron apoptotic process / mitochondrial fusion / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / epithelial cell apoptotic process / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / germ cell development / negative regulation of mitochondrial membrane potential / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / negative regulation of apoptotic signaling pathway / B cell homeostasis / 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 / blood vessel remodeling / ectopic germ cell programmed cell death / cellular response to unfolded protein / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to gamma radiation / neuron migration / cerebral cortex development / response to toxic substance / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to UV
Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / 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 ...Poxvirus F1/C10 / Apoptosis regulator M11L like / 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
Similarity search - Domain/homology
anti-apoptotic membrane protein / Apoptosis regulator BAX
Similarity search - Component
Biological speciesSheeppox virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91414639113 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1007918 Australia
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structures of the sheeppox virus encoded inhibitor of apoptosis SPPV14 bound to the proapoptotic BH3 peptides Hrk and Bax.
Authors: Suraweera, C.D. / Burton, D.R. / Hinds, M.G. / Kvansakul, M.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-apoptotic membrane protein
B: Apoptosis regulator BAX
C: anti-apoptotic membrane protein
D: Apoptosis regulator BAX
E: anti-apoptotic membrane protein
F: Apoptosis regulator BAX
G: anti-apoptotic membrane protein
H: Apoptosis regulator BAX
I: anti-apoptotic membrane protein
J: Apoptosis regulator BAX
K: anti-apoptotic membrane protein
L: Apoptosis regulator BAX
M: anti-apoptotic membrane protein
N: Apoptosis regulator BAX
O: anti-apoptotic membrane protein
P: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)162,56016
Polymers162,56016
Non-polymers00
Water70339
1
A: anti-apoptotic membrane protein
B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,6292
Polymers20,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-15 kcal/mol
Surface area8780 Å2
MethodPISA
2
C: anti-apoptotic membrane protein
D: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,2172
Polymers20,2172
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-16 kcal/mol
Surface area9070 Å2
MethodPISA
3
E: anti-apoptotic membrane protein
F: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,2172
Polymers20,2172
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-17 kcal/mol
Surface area8770 Å2
MethodPISA
4
G: anti-apoptotic membrane protein
H: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,6292
Polymers20,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-18 kcal/mol
Surface area8600 Å2
MethodPISA
5
I: anti-apoptotic membrane protein
J: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,2172
Polymers20,2172
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-16 kcal/mol
Surface area8400 Å2
MethodPISA
6
K: anti-apoptotic membrane protein
L: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,2172
Polymers20,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-16 kcal/mol
Surface area8690 Å2
MethodPISA
7
M: anti-apoptotic membrane protein
N: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,2172
Polymers20,2172
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-17 kcal/mol
Surface area8500 Å2
MethodPISA
8
O: anti-apoptotic membrane protein
P: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)20,2172
Polymers20,2172
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-15 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.279, 78.560, 107.766
Angle α, β, γ (deg.)90.000, 110.968, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72
82

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 6 through 37 or resid 39 through 137))A6 - 37
121(chain 'A' and (resid 6 through 37 or resid 39 through 137))A39 - 137
231(chain 'C' and (resid 6 through 37 or resid 39 through 137))C6 - 37
241(chain 'C' and (resid 6 through 37 or resid 39 through 137))C39 - 137
351(chain 'E' and (resid 6 through 37 or resid 39 through 137))E6 - 37
361(chain 'E' and (resid 6 through 37 or resid 39 through 137))E39 - 137
471(chain 'G' and (resid 6 through 37 or resid 39 through 137))G6 - 37
481(chain 'G' and (resid 6 through 37 or resid 39 through 137))G39 - 137
591(chain 'I' and (resid 6 through 37 or resid 39 through 137))I6 - 37
5101(chain 'I' and (resid 6 through 37 or resid 39 through 137))I39 - 137
6111(chain 'K' and (resid 6 through 37 or resid 39 through 137))K6 - 37
6121(chain 'K' and (resid 6 through 37 or resid 39 through 137))K39 - 137
7131(chain 'M' and (resid 6 through 37 or resid 39 through 137))M6 - 37
7141(chain 'M' and (resid 6 through 37 or resid 39 through 137))M39 - 137
8151(chain 'O' and (resid 6 through 37 or resid 39 through 137))O6 - 37
8161(chain 'O' and (resid 6 through 37 or resid 39 through 137))O39 - 137
1172(chain 'B' and resid 54 through 73)B54 - 73
2182(chain 'D' and resid 54 through 73)D54 - 73
3192(chain 'F' and resid 54 through 73)F54 - 73
4202(chain 'H' and resid 54 through 73)H54 - 73
5212(chain 'J' and resid 54 through 73)J54 - 73
6222(chain 'L' and resid 54 through 73)L54 - 73
7232(chain 'N' and resid 54 through 73)N54 - 73
8242(chain 'P' and resid 54 through 73)P54 - 73

NCS ensembles :
ID
1
2

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Components

#1: Protein anti-apoptotic membrane protein


Mass: 17476.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sheeppox virus (strain Turkey/TU-V02127)
Gene: SPPV_14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A3F2YKH3
#2: Protein/peptide
Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 3152.553 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812
#3: Protein
anti-apoptotic membrane protein


Mass: 17064.570 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sheeppox virus (strain Turkey/TU-V02127)
Gene: SPPV_14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A3F2YKH3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.0 M Lithium chloride, 0.1 M Citrate pH 4.0, 20% w/vPEG 6000

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.91→46.8192839353 Å / Num. obs: 34323 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.2386465218 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.2
Reflection shellResolution: 2.91→3.06 Å / Rmerge(I) obs: 1.244 / Num. unique obs: 4465 / CC1/2: 0.545

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Processing

Software
NameVersionClassification
Coot0.8.0-3model building
PHENIX1.11.1_2575refinement
XDS20180427data reduction
Aimless7data scaling
PHASER1.11.1-2575-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SPPV_Hrk

Resolution: 2.91414639113→46.8192839353 Å / SU ML: 0.536279074799 / Cross valid method: FREE R-VALUE / σ(F): 1.34422129548 / Phase error: 33.0426813257
RfactorNum. reflection% reflection
Rfree0.288336241435 1784 5.20982390562 %
Rwork0.238579484104 --
obs0.241186273945 34243 99.3270485859 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.91 Å2
Refinement stepCycle: LAST / Resolution: 2.91414639113→46.8192839353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10275 0 0 44 10319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039185532225410355
X-RAY DIFFRACTIONf_angle_d0.63380988893413904
X-RAY DIFFRACTIONf_chiral_restr0.04145259511961659
X-RAY DIFFRACTIONf_plane_restr0.003594314065461776
X-RAY DIFFRACTIONf_dihedral_angle_d15.98436527716582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91414639113-2.9920.3905624964911400.3520628022732381X-RAY DIFFRACTION96.3685015291
2.9929-3.0810.3730573897381490.3347537763282492X-RAY DIFFRACTION99.6603773585
3.081-3.18040.3974607905481260.3360178313672499X-RAY DIFFRACTION99.6961640714
3.1804-3.2940.4024006253561460.3240914713522474X-RAY DIFFRACTION99.8095238095
3.294-3.42590.3370778299591210.2930742103552523X-RAY DIFFRACTION99.8112495281
3.4259-3.58180.3371819364141440.280701792132491X-RAY DIFFRACTION99.5090634441
3.5818-3.77050.2973937788081190.2581182688892473X-RAY DIFFRACTION99.27230946
3.7705-4.00660.263593640481130.2309092220162541X-RAY DIFFRACTION99.7744360902
4.0066-4.31580.2389135524931450.2007448289882505X-RAY DIFFRACTION100
4.3158-4.74970.2676113209531470.1920050931552493X-RAY DIFFRACTION99.7732426304
4.7497-5.43610.2691442706681390.2162746858142511X-RAY DIFFRACTION99.7365449755
5.4361-6.84550.3059572689551520.2606342744222513X-RAY DIFFRACTION99.7007108118

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