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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tqq
TitleStructural insight into tanapoxvirus mediated inhibition of apoptosis
Components
  • 16L protein
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Pox virus / Bcl-2
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / : / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / : / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / tube formation / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / regulation of organ growth / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / cell-matrix adhesion / post-embryonic development / thymus development / kidney development / positive regulation of protein-containing complex assembly / male gonad development / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / microtubule binding / spermatogenesis / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / molecular adaptor activity / positive regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / membrane / cytosol
Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2-like protein 11 / 16L protein
Similarity search - Component
Biological speciesYaba-like disease virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.00179724185 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-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7403
Polymers20,7172
Non-polymers231
Water1448
1
A: 16L protein
B: Bcl-2-like protein 11
hetero molecules

A: 16L protein
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4806
Polymers41,4344
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area9350 Å2
ΔGint-94 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.654, 59.654, 90.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein 16L protein


Mass: 17442.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Viral Bcl-2 homolog in Tanapox virus / 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-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3274.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BH3 motif of Bcl-2-like protein 11 (BIM) / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#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.: 8 / 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: 2.2 Å3/Da / Density % sol: 44.01 % / Description: Small cubic shape single crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MIB pH 8.0, 25% PEG 1500

-
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: 3→51.6622258475 Å / Num. obs: 4030 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 86.2771477384 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.3
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.168 / Num. unique obs: 4030 / CC1/2: 0.996 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHASER1.11.1_2575phasing
XDSdata reduction
Aimless7.0.077data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Previously solved structure of TNP_Bax

Resolution: 3.00179724185→51.6622258475 Å / SU ML: 0.416669645544 / Cross valid method: FREE R-VALUE / σ(F): 1.34348368526 / Phase error: 21.9622995312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.276375214102 211 5.26315789474 %
Rwork0.242231925533 3798 -
obs0.243997220214 4009 99.8256972112 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.0484228492 Å2
Refinement stepCycle: LAST / Resolution: 3.00179724185→51.6622258475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 1 8 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003292724199211314
X-RAY DIFFRACTIONf_angle_d0.5539385250031763
X-RAY DIFFRACTIONf_chiral_restr0.0363384959154203
X-RAY DIFFRACTIONf_plane_restr0.00355298483034223
X-RAY DIFFRACTIONf_dihedral_angle_d15.5290751998828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0018-3.78180.341073634672910.2758223333791861X-RAY DIFFRACTION99.8976458547
3.7818-51.6622250.2619435253441200.2302317438271937X-RAY DIFFRACTION99.7575169738
Refinement TLS params.Method: refined / Origin x: -10.9210480167 Å / Origin y: 41.8274946086 Å / Origin z: 95.3140751365 Å
111213212223313233
T0.369618422922 Å2-0.0368418913202 Å2-0.025918069006 Å2-0.389130668158 Å2-0.027985005639 Å2--0.366149412353 Å2
L0.592186852537 °20.206902629794 °2-0.224175480508 °2-2.53035222931 °20.511074171571 °2--1.56183979355 °2
S0.0124048822673 Å °0.0545475403707 Å °0.0263075918637 Å °-0.175984778348 Å °-0.160693117809 Å °-0.0687473076326 Å °0.187948160071 Å °-0.0882600732321 Å °-2.74569332755E-5 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