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- PDB-2jby: A viral protein unexpectedly mimics the structure and function of... -

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Basic information

Entry
Database: PDB / ID: 2jby
TitleA viral protein unexpectedly mimics the structure and function of pro- survival Bcl-2
Components
  • BCL-2 HOMOLOGOUS ANTAGONIST/KILLER 2
  • M11L PROTEIN
KeywordsAPOPTOSIS
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / pore complex / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / regulation of apoptotic process / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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. ...Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Bcl-2 homologous antagonist/killer / Apoptosis regulator M11L
Similarity search - Component
Biological speciesMYXOMA VIRUS
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.41 Å
AuthorsKvansakul, M. / Van Delft, M.F. / Lee, E.F. / Gulbis, J.M. / Fairlie, W.D. / Huang, D.C.S. / Colman, P.M.
CitationJournal: Mol. Cell / Year: 2007
Title: A structural viral mimic of prosurvival Bcl-2: a pivotal role for sequestering proapoptotic Bax and Bak.
Authors: Kvansakul, M. / van Delft, M.F. / Lee, E.F. / Gulbis, J.M. / Fairlie, W.D. / Huang, D.C. / Colman, P.M.
History
DepositionDec 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 13, 2018Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M11L PROTEIN
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5053
Polymers19,4822
Non-polymers231
Water1,04558
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-24.3 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.187, 69.187, 120.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein M11L PROTEIN / APOPTOSIS REGULATOR M11L / M11L


Mass: 16599.957 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYXOMA VIRUS / Strain: LAUSANNE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYS / References: UniProt: Q85295
#2: Protein/peptide BCL-2 HOMOLOGOUS ANTAGONIST/KILLER 2 / APOPTOSIS REGULATOR BAK-2 / BAK


Mass: 2882.151 Da / Num. of mol.: 1 / Fragment: BH3 DOMAIN, RESIDUES 67-92 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q13014, UniProt: Q16611*PLUS
#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


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.88 % / Description: NONE
Crystal growpH: 7.5 / Details: 2.4 M (NH4)2HPO4, 50MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.99
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 11933 / % possible obs: 93.8 % / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 59.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.41→20 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.895 / SU B: 24.057 / SU ML: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM SG IN CYS28 CHAIN A APPEARS MOSTLY DISORDERED AND HAS BEEN ASSIGNED AN OCCUPANCY OF 0.2.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1089 9.7 %RANDOM
Rwork0.287 ---
obs0.288 10139 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2--1.31 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.41→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 1 58 1260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9691585
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.38726.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36115212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.31153
X-RAY DIFFRACTIONr_chiral_restr0.2420.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02853
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2770.2612
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2836
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3760.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5210.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4462753
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70331216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2536425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.846369
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.428 39
Rwork0.312 459
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)
14.03760.6083-0.76611.3246-0.92912.23930.0339-0.0705-0.1263-0.1609-0.0967-0.0846-0.24480.17110.06280.0621-0.01860.0568-0.2264-0.0369-0.257539.022376.9022-15.4136
25.07012.23242.291315.96343.52778.674-0.9134-0.3493-1.80880.47360.0929-0.12470.90771.60390.82050.2360.03880.0294-0.15640.21950.086741.256663.85-10.5301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 128
2X-RAY DIFFRACTION1A1129
3X-RAY DIFFRACTION1A2001 - 2043
4X-RAY DIFFRACTION1B2001 - 2015
5X-RAY DIFFRACTION2B68 - 92

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