[English] 日本語
Yorodumi
- PDB-6tqp: Structural insight into tanapoxvirus mediated inhibition of apoptosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tqp
TitleStructural insight into tanapoxvirus mediated inhibition of apoptosis
Components
  • 16L protein
  • Bcl-2-binding component 3, isoforms 1/2
KeywordsAPOPTOSIS / Pox virus / Bcl-2
Function / homology
Function and homology information


positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / execution phase of apoptosis ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / Activation of PUMA and translocation to mitochondria / FOXO-mediated transcription of cell death genes / 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 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / cellular response to ionizing radiation / determination of adult lifespan / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to hypoxia / regulation of apoptotic process / mitochondrial outer membrane / DNA damage response / mitochondrion / membrane / cytosol
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Poxvirus F1/C10 / Apoptosis regulator M11L like / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2-binding component 3, isoforms 1/2 / 16L protein
Similarity search - Component
Biological speciesYaba-like disease virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8494094828 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 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 1, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16L protein
B: Bcl-2-binding component 3, isoforms 1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6763
Polymers20,6532
Non-polymers231
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-18 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.093, 54.869, 60.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
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 homologe / Source: (gene. exp.) Yaba-like disease virus / Gene: 16L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9DHU6
#2: Protein/peptide Bcl-2-binding component 3, isoforms 1/2 / JFY-1 / p53 up-regulated modulator of apoptosis


Mass: 3210.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PUMA BH3 motif (26-mer) / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.34 % / Description: long rod shape crystals with sharp edges
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Potassium thiocyanate, 30% PEG 2000MME

-
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: 1.849→32.45 Å / Num. obs: 15799 / % possible obs: 99.51 % / Redundancy: 5.5 % / Biso Wilson estimate: 36.7645901849 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.1
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 / Num. unique obs: 15850 / CC1/2: 0.998 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDS1.11.1_2575data reduction
Aimless7.0.077data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: previously solved structure of TNP_16L

Resolution: 1.8494094828→32.4499523192 Å / SU ML: 0.297080171611 / Cross valid method: FREE R-VALUE / σ(F): 1.33787641762 / Phase error: 28.0186733218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218444012118 762 4.82309006899 %
Rwork0.190904044812 15037 -
obs0.192246521962 15799 99.5275292932 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.7601363343 Å2
Refinement stepCycle: LAST / Resolution: 1.8494094828→32.4499523192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 1 91 1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00579015982311383
X-RAY DIFFRACTIONf_angle_d0.6866284756361854
X-RAY DIFFRACTIONf_chiral_restr0.0408329905669211
X-RAY DIFFRACTIONf_plane_restr0.00368233399179238
X-RAY DIFFRACTIONf_dihedral_angle_d12.1678602204878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8494094828-1.99220.377856447411530.3037875144552932X-RAY DIFFRACTION98.6884197057
1.9922-2.19260.229728639041450.2256881558392969X-RAY DIFFRACTION99.7437540038
2.1926-2.50980.2480920832191640.1836672117922972X-RAY DIFFRACTION99.8408150271
2.5098-3.16170.2092838719391380.2013311600033025X-RAY DIFFRACTION99.6848408446
3.1617-32.44995231920.2000317966961620.1738845013233139X-RAY DIFFRACTION99.6678743961
Refinement TLS params.Method: refined / Origin x: 36.5450173979 Å / Origin y: 30.7032327682 Å / Origin z: 18.4936300547 Å
111213212223313233
T0.265130984436 Å2-0.00605318759539 Å20.0305690426312 Å2-0.231880351417 Å2-0.0286063225778 Å2--0.240356904338 Å2
L2.82349854535 °2-0.73372314829 °21.27623313424 °2-2.47648264423 °2-0.679833865343 °2--3.00450345371 °2
S0.00635052288095 Å °0.0407511797172 Å °0.132736422958 Å °0.0626038354049 Å °-0.0468402123168 Å °-0.0474441772842 Å °-0.0562598930567 Å °0.0818853986076 Å °0.0380219783688 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more