[English] 日本語
Yorodumi
- PDB-5ua4: Crystal structure of A179L:Bid BH3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ua4
TitleCrystal structure of A179L:Bid BH3 complex
Components
  • 5-HL
  • BH3-interacting domain death agonist
KeywordsAPOPTOSIS / Bcl-2
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / Activation, translocation and oligomerization of BAX / : / suppression by virus of host autophagy / positive regulation of extrinsic apoptotic signaling pathway / host cell endoplasmic reticulum / apoptotic mitochondrial changes / positive regulation of release of cytochrome c from mitochondria / host cell mitochondrion ...Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / Activation, translocation and oligomerization of BAX / : / suppression by virus of host autophagy / positive regulation of extrinsic apoptotic signaling pathway / host cell endoplasmic reticulum / apoptotic mitochondrial changes / positive regulation of release of cytochrome c from mitochondria / host cell mitochondrion / positive regulation of intrinsic apoptotic signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of apoptotic process / mitochondrial outer membrane / mitochondrion / cytosol
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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 ...BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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
Apoptosis regulator Bcl-2 homolog / Apoptosis regulator Bcl-2 homolog / BH3-interacting domain death agonist
Similarity search - Component
Biological speciesAfrican swine fever virus
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBanjara, S. / Caria, S. / 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: J. Virol. / Year: 2017
Title: Structural Insight into African Swine Fever Virus A179L-Mediated Inhibition of Apoptosis.
Authors: Banjara, S. / Caria, S. / Dixon, L.K. / Hinds, M.G. / Kvansakul, M.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Mar 15, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-HL
B: BH3-interacting domain death agonist


Theoretical massNumber of molelcules
Total (without water)21,5402
Polymers21,5402
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-15 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.761, 48.778, 56.535
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number5
Space group name H-MC121
DetailsDimer as determined by size exclusion chromatography

-
Components

#1: Protein 5-HL / A179L / Bcl-2-like protein / PA179L


Mass: 17709.230 Da / Num. of mol.: 1 / Fragment: residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: 5-HL, A179L / Production host: Escherichia coli (E. coli) / References: UniProt: D0Q0E8, UniProt: P42485*PLUS
#2: Protein/peptide BH3-interacting domain death agonist


Mass: 3830.336 Da / Num. of mol.: 1 / Fragment: residues 73-106 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig) / References: UniProt: Q4JHS0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.1 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 27.5% (w/v) PEG 4000, 0.11 M, Ammonium sulphate and 0.1 M Sodium cacodylate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→39.11 Å / Num. obs: 5150 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.5 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.11 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.33
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 253 4.91 %Random selection
Rwork0.2161 ---
obs0.2183 5148 92.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 20 1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051396
X-RAY DIFFRACTIONf_angle_d0.8681888
X-RAY DIFFRACTIONf_dihedral_angle_d15.789510
X-RAY DIFFRACTIONf_chiral_restr0.03212
X-RAY DIFFRACTIONf_plane_restr0.004237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-3.27550.31171280.26462455X-RAY DIFFRACTION94
3.2755-39.110.23641250.19312440X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00480.00470.05690.01030.03420.91550.0224-0.2187-0.0613-0.0270.14540.3567-0.9508-0.4928-0.01490.33370.09110.01960.33840.03410.397613.340642.796113.033
21.75370.28591.08560.28460.11470.6998-0.2466-0.24740.17480.0866-0.19470.2146-0.5056-0.0578-0.22590.7206-0.19240.10560.5188-0.15670.2123.484545.32859.1677
30.5387-0.07080.77150.0418-0.30922.4856-0.6110.0189-0.25820.14790.0392-0.4468-0.36041.1844-0.03020.4115-0.0119-0.05940.3319-0.07780.569820.337250.57416.8336
40.7271-0.3381-0.29681.58590.12660.46220.02780.1126-0.1006-0.5707-0.01350.4075-0.0281-0.0844-0.04120.3014-0.0026-0.05750.23670.01380.207216.340132.151211.5062
50.1720.03450.14431.7106-0.48640.2960.2514-0.15220.5901-0.11840.12210.5754-0.2148-0.31750.62790.04770.00960.11910.37570.03120.51915.67737.631423.6066
61.3042-0.8949-0.48132.9179-2.22133.65450.1238-0.15620.1036-0.44910.21330.19180.56550.2370.94350.1769-0.0050.00650.24730.08820.240416.661921.349417.6611
71.67911.9999-1.38182.4733-1.47831.42780.4907-0.2146-0.05150.6484-0.4498-0.4741-0.17180.3466-0.25760.3646-0.01980.05680.2827-0.00450.321421.10222.775538.4454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 143 )
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 46 )
7X-RAY DIFFRACTION7chain 'B' and (resid 47 through 57 )

+
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://pdbjlvh1.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