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- PDB-4d2l: Vaccinia Virus F1L bound to Bak BH3 -

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Basic information

Entry
Database: PDB / ID: 4d2l
TitleVaccinia Virus F1L bound to Bak BH3
Components
  • BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
  • PROTEIN F1L
KeywordsAPOPTOSIS / BIM / BAK
Function / homology
Function and homology information


host cell mitochondrial outer membrane / 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 ...host cell mitochondrial outer membrane / 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 / Pyroptosis / animal organ regeneration / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / 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
Orthopoxvirus protein F1 / 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 ...Orthopoxvirus protein F1 / 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
Apoptosis regulator OPG045 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesVACCINIA VIRUS
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsKvansakul, M. / Colman, P.M.
CitationJournal: J.Virol. / Year: 2014
Title: Structural Insight Into Bh3-Domain Binding of Vaccinia Virus Anti-Apoptotic F1L.
Authors: Campbell, S. / Thibault, J. / Mehta, N. / Colman, P.M. / Barry, M. / Kvansakul, M.
History
DepositionMay 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN F1L
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER


Theoretical massNumber of molelcules
Total (without water)24,4302
Polymers24,4302
Non-polymers00
Water00
1
A: PROTEIN F1L
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER

A: PROTEIN F1L
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER


Theoretical massNumber of molelcules
Total (without water)48,8594
Polymers48,8594
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Buried area9170 Å2
ΔGint-82.1 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.691, 116.691, 103.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein PROTEIN F1L


Mass: 21490.262 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-186 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS (STRAIN ANKARA) (VACV) / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: O57173
#2: Protein/peptide BCL-2 HOMOLOGOUS ANTAGONIST/KILLER / APOPTOSIS REGULATOR BAK / BCL-2-LIKE PROTEIN 7 / BCL2-L-7 / F1L


Mass: 2939.268 Da / Num. of mol.: 1 / Fragment: RESIDUES 67-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: Q16611
Sequence detailsI125F MUTATION WAS INTRODUCED

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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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.18 M AMMONIUM SULFATE AND 2.25 M LICL., pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.9→38.74 Å / Num. obs: 9630 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 92.23 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39.6
Reflection shellHighest resolution: 2.9 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VTY

2vty


Resolution: 2.903→38.745 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 454 4.7 %
Rwork0.2013 --
obs0.2025 9605 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.903→38.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 0 1309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011327
X-RAY DIFFRACTIONf_angle_d1.261789
X-RAY DIFFRACTIONf_dihedral_angle_d16.179502
X-RAY DIFFRACTIONf_chiral_restr0.049206
X-RAY DIFFRACTIONf_plane_restr0.005227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9032-3.32320.30461550.26222976X-RAY DIFFRACTION100
3.3232-4.1860.21681520.21683013X-RAY DIFFRACTION100
4.186-38.7480.21741470.18353162X-RAY DIFFRACTION98
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)
10.3999-0.89380.20891.894-0.45360.0959-0.0566-1.4698-2.96862.14890.0693-0.0137-0.41591.3306-0.00571.4681-0.21260.25391.12290.15171.144528.275-36.5650.7741
21.64131.3908-1.45823.47141.47453.290.98380.32950.38570.0075-0.43870.64380.30220.1512-1.75490.99990.04240.19340.90380.19170.983926.8484-31.8142-16.0288
34.29920.7474-0.15271.8230.15852.41750.14420.23470.09740.21430.05990.4021-0.1583-0.2515-0.00340.74060.01190.14080.9189-0.05930.79117.6939-46.5591-12.6541
42.9006-1.1532-2.40791.6839-2.16032.9630.6330.24780.37640.1846-0.12850.0713-0.2869-0.49660.00810.62490.00050.10050.8769-0.01170.757710.7787-46.6103-16.1772
50.5313-0.1484-0.46361.2697-0.07220.48180.8205-2.1575-1.2647-0.97540.57070.51041.3818-1.63940.01880.8499-0.11970.00611.13270.23011.05811.5725-52.8084-6.0837
60.125-0.18560.30010.2642-0.32080.4754-0.0745-0.52961.3556-1.6877-0.11240.0641-0.4591-0.51350.02431.35660.46230.40671.89570.32671.5422-9.9526-42.4904-12.0823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 49 THROUGH 57 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 58 THROUGH 80 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 81 THROUGH 139 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 140 THROUGH 186 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 54 THROUGH 70 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 71 THROUGH 76 )

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