[English] 日本語
Yorodumi
- PDB-3bl2: Crystal Structure of M11, the BCL-2 Homolog of Murine Gamma-herpe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bl2
TitleCrystal Structure of M11, the BCL-2 Homolog of Murine Gamma-herpesvirus 68, Complexed with Mouse Beclin1 (residues 106-124)
Components
  • Beclin-1
  • V-bcl-2
KeywordsVIRAL PROTEIN/APOPTOSIS / protein-protein complex / viral BCL-2 / Beclin1 / apoptosis / M11 / autophagy / Antiviral defense / Coiled coil / Cytoplasm / Golgi apparatus / Membrane / VIRAL PROTEIN-APOPTOSIS COMPLEX
Function / homology
Function and homology information


Macroautophagy / cellular response to aluminum ion / ISG15 antiviral mechanism / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore ...Macroautophagy / cellular response to aluminum ion / ISG15 antiviral mechanism / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / engulfment of apoptotic cell / suppression by virus of host autophagy / protein targeting to lysosome / early endosome to late endosome transport / late endosome to vacuole transport / response to other organism / cellular response to nitrogen starvation / SMAD protein signal transduction / Ub-specific processing proteases / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / phosphatidylinositol-3-phosphate biosynthetic process / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / lysosome organization / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / mitophagy / autophagosome maturation / autophagosome assembly / negative regulation of reactive oxygen species metabolic process / neuron development / autophagosome / response to vitamin E / regulation of macroautophagy / amyloid-beta metabolic process / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / phagocytic vesicle / negative regulation of autophagy / regulation of cytokinesis / regulation of autophagy / macroautophagy / response to lead ion / trans-Golgi network / autophagy / cellular response to hydrogen peroxide / GTPase binding / protein-macromolecule adaptor activity / cytoplasmic vesicle / protein-containing complex assembly / regulation of apoptotic process / angiogenesis / defense response to virus / host cell cytoplasm / cytoskeleton / nuclear body / endosome membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / apoptotic process / ubiquitin protein ligase binding / dendrite / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator M11 / Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region ...Apoptosis regulator M11 / Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Beclin-1 / Apoptosis regulator Bcl-2 homolog
Similarity search - Component
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsOh, B.-H. / Woo, J.-S. / Ku, B.
CitationJournal: Plos Pathog. / Year: 2008
Title: Structural and Biochemical Bases for the Inhibition of Autophagy and Apoptosis by Viral BCL-2 of Murine gamma-Herpesvirus 68
Authors: Ku, B. / Woo, J.-S. / Liang, C. / Lee, K.-H. / Hong, H.-S. / E, X. / Kim, K.-S. / Jung, J.U. / Oh, B.-H.
History
DepositionDec 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: 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: V-bcl-2
B: V-bcl-2
C: Beclin-1
D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)34,7904
Polymers34,7904
Non-polymers00
Water1,06359
1
A: V-bcl-2
C: Beclin-1


Theoretical massNumber of molelcules
Total (without water)17,3952
Polymers17,3952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
MethodPISA
2
B: V-bcl-2
D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)17,3952
Polymers17,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
MethodPISA
3
A: V-bcl-2
C: Beclin-1

B: V-bcl-2
D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)34,7904
Polymers34,7904
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area5130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.863, 53.601, 73.586
Angle α, β, γ (deg.)90.000, 107.540, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein V-bcl-2 / Bcl-2 homolog / Gene 16? / M11


Mass: 15152.237 Da / Num. of mol.: 2 / Fragment: UNP residues 5-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Gene: v-bcl-2, GAMMAHV.M11, M11 / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P89884
#2: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein


Mass: 2242.639 Da / Num. of mol.: 2
Fragment: BCL-2 binding region, BH3-like domain, UNP residues 106-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Becn1 / Plasmid: pPROEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O88597
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 13513 / % possible obs: 94 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.582 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.383.30.16211501.46380.5
2.38-2.483.50.14212101.44586.1
2.48-2.593.70.13912911.45690.2
2.59-2.7340.1313431.63593.3
2.73-2.94.30.10613651.52495.1
2.9-3.124.70.0913971.54597.5
3.12-3.435.80.07214071.51598.7
3.43-3.935.90.0614311.75699.4
3.93-4.956.40.04614451.59799.2
4.95-306.20.04414741.64899.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.05 Å29.33 Å
Translation3.05 Å29.33 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABO

2abo


Resolution: 2.3→20 Å / FOM work R set: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 684 4.8 %RANDOM
Rwork0.204 ---
obs-13447 94.1 %-
Solvent computationBsol: 32.021 Å2
Displacement parametersBiso mean: 29.914 Å2
Baniso -1Baniso -2Baniso -3
1--7.076 Å20 Å211.09 Å2
2--3.283 Å20 Å2
3---3.793 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 0 59 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.0627
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5531.5
X-RAY DIFFRACTIONc_mcangle_it2.6572
X-RAY DIFFRACTIONc_scbond_it2.2672
X-RAY DIFFRACTIONc_scangle_it3.3662.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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