[English] 日本語
Yorodumi
- PDB-6xy4: Structural insight into sheep-pox virus mediated inhibition of ap... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xy4
TitleStructural insight into sheep-pox virus mediated inhibition of apoptosis
Components
  • Activator of apoptosis harakiri
  • anti-apoptotic membrane protein
KeywordsAPOPTOSIS / Pox virus / Bcl-2
Function / homology
Function and homology information


: / positive regulation of release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / positive regulation of apoptotic process / apoptotic process / mitochondrion / membrane
Similarity search - Function
Activator of apoptosis harakiri / Activator of apoptosis harakiri / Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Bcl-2-like superfamily
Similarity search - Domain/homology
anti-apoptotic membrane protein / Activator of apoptosis harakiri
Similarity search - Component
Biological speciesSheeppox virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04623155256 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
Revision 1.1Jan 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: anti-apoptotic membrane protein
B: Activator of apoptosis harakiri


Theoretical massNumber of molelcules
Total (without water)20,4492
Polymers20,4492
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-19 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.280, 70.660, 115.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein anti-apoptotic membrane protein


Mass: 17476.027 Da / Num. of mol.: 1
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 Activator of apoptosis harakiri / BH3-interacting domain-containing protein 3 / Neuronal death protein DP5


Mass: 2973.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00198
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/vPEG 3350

-
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: 2.046→31.07 Å / Num. obs: 11236 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 39.8950367928 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.7
Reflection shellResolution: 2.05→8.92 Å / Num. unique obs: 782 / CC1/2: 0.573

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Coot0.8.0-3model building
XDS20180427data reduction
Aimless7data scaling
PHASER1.11.1_2575-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJY

2bjy


Resolution: 2.04623155256→31.0657632133 Å / SU ML: 0.237702211781 / Cross valid method: FREE R-VALUE / σ(F): 1.38553218358 / Phase error: 26.211733487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233810671103 568 5.05517977928 %
Rwork0.219930444744 10668 -
obs0.220603579671 11236 97.6958525346 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.7478958779 Å2
Refinement stepCycle: LAST / Resolution: 2.04623155256→31.0657632133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 28 1257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002384084319851245
X-RAY DIFFRACTIONf_angle_d0.3977592978351673
X-RAY DIFFRACTIONf_chiral_restr0.0332360412731200
X-RAY DIFFRACTIONf_plane_restr0.00140794756101211
X-RAY DIFFRACTIONf_dihedral_angle_d16.9358529231787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04623155265-2.25210.2731022405161590.2573813541462523X-RAY DIFFRACTION95.0726692662
2.2521-2.57780.2591322272281220.2397820022942689X-RAY DIFFRACTION99.1534391534
2.5778-3.24730.2500136083211530.2366133398562677X-RAY DIFFRACTION98.812849162
3.2473-31.06576321330.215540740211340.2040902909842779X-RAY DIFFRACTION97.7188862798
Refinement TLS params.Method: refined / Origin x: -18.4590111381 Å / Origin y: -12.5771924003 Å / Origin z: -11.1701382726 Å
111213212223313233
T0.356873017009 Å20.0201448405319 Å20.0175253669372 Å2-0.344584880018 Å20.0014601194472 Å2--0.341014260961 Å2
L4.45340416183 °21.53913903174 °20.823391120508 °2-2.58557950292 °2-0.853219529095 °2--4.65257779361 °2
S-0.0564594308793 Å °0.365321035451 Å °0.0211249438113 Å °-0.278965474825 Å °0.153017389009 Å °0.0900464395735 Å °0.0812525005108 Å °-0.05125301716 Å °0.00420459506247 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