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- PDB-6trr: Structural insight into tanapoxvirus mediated inhibition of apoptosis -

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Basic information

Entry
Database: PDB / ID: 6trr
TitleStructural insight into tanapoxvirus mediated inhibition of apoptosis
Components
  • 16L protein
  • 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 / 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 / symbiont-mediated suppression of host apoptosis / 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
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...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-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
Apoptosis regulator BAX / 16L protein
Similarity search - Component
Biological speciesYaba-like disease virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1200735104 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 J. / Year: 2020
Title: Structural insight into tanapoxvirus-mediated inhibition of apoptosis.
Authors: Suraweera, C.D. / Anasir, M.I. / Chugh, S. / Javorsky, A. / Impey, R.E. / Hasan Zadeh, M. / Soares da Costa, T.P. / Hinds, M.G. / Kvansakul, M.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Jan 24, 2024Group: 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: 16L protein
B: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6414
Polymers20,5952
Non-polymers462
Water46826
1
A: 16L protein
B: Apoptosis regulator BAX
hetero molecules

A: 16L protein
B: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2828
Polymers41,1904
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9550 Å2
ΔGint-109 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.376, 55.376, 126.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein 16L protein


Mass: 17442.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Tanapox virus Bcl-2 protein / Source: (gene. exp.) Yaba-like disease virus / Gene: 16L / Cell line (production host): C41 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DHU6
#2: Protein/peptide Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 3152.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BH3 motif of Human Bax protein / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.29 Å3/Da / Density % sol: 46.24 % / Description: single square bipyramidal shape crystals
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% PEG 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: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.12→42.31 Å / Num. obs: 11903 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 50.7844344791 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.2
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 946 / CC1/2: 0.291

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Processing

Software
NameVersionClassification
PHASER1.11.1_2575phasing
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless7.0.077data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UF1

4uf1


Resolution: 2.1200735104→33.6224352648 Å / SU ML: 0.307808956948 / Cross valid method: FREE R-VALUE / σ(F): 1.33600998648 / Phase error: 30.2921234659
RfactorNum. reflection% reflection
Rfree0.254194038733 607 5.12712222316 %
Rwork0.239581886093 --
obs0.240417513652 11839 99.9071729958 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.773837679 Å2
Refinement stepCycle: LAST / Resolution: 2.1200735104→33.6224352648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 2 26 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028435348091317
X-RAY DIFFRACTIONf_angle_d0.435621515771766
X-RAY DIFFRACTIONf_chiral_restr0.0353068282197208
X-RAY DIFFRACTIONf_plane_restr0.00319314991276223
X-RAY DIFFRACTIONf_dihedral_angle_d16.4554221309848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1201-2.33340.3290808827861390.3101667467222743X-RAY DIFFRACTION99.7577016269
2.3334-2.67090.319447436991700.2792247065352717X-RAY DIFFRACTION100
2.6709-3.36460.2810851677931440.2591184405122799X-RAY DIFFRACTION99.8981670061
3.3646-33.62243526480.225699731331540.2189481418632973X-RAY DIFFRACTION99.9680306905
Refinement TLS params.Method: refined / Origin x: 3.63385323757 Å / Origin y: 8.30386774601 Å / Origin z: 20.5216577962 Å
111213212223313233
T0.26617437887 Å20.0262934132777 Å2-0.0410971348907 Å2-0.578234959464 Å20.0353140885973 Å2--0.485470312784 Å2
L1.48687738743 °20.509109240692 °2-1.36966606062 °2-2.62941748525 °2-0.812340911753 °2--3.60692482469 °2
S-0.0914401365323 Å °0.280849636319 Å °0.0418961203884 Å °0.0278821065165 Å °0.0197845704056 Å °-0.0950548656585 Å °0.0834005835269 Å °-0.0129704770893 Å °0.0438796510864 Å °
Refinement TLS groupSelection details: all

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