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- PDB-5ajj: Crystal structure of variola virus virulence factor F1L in comple... -

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Basic information

Entry
Database: PDB / ID: 5ajj
TitleCrystal structure of variola virus virulence factor F1L in complex with human Bid BH3 domain
Components
  • BH3-INTERACTING DOMAIN DEATH AGONIST
  • HOMOLOG OF VACCINIA VIRUS CDS F1L PUTATIVE
KeywordsVIRAL PROTEIN / BCL-2 / APOPTOSIS / POXVIRUS / BID
Function / homology
Function and homology information


cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / host cell mitochondrial outer membrane / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / : / positive regulation of fibroblast apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / host cell mitochondrial outer membrane / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / : / positive regulation of fibroblast apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to mitochondrion / regulation of epithelial cell proliferation / establishment of protein localization to membrane / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / mitochondrial ATP synthesis coupled electron transport / regulation of T cell proliferation / hepatocyte apoptotic process / apoptotic mitochondrial changes / regulation of G1/S transition of mitotic cell cycle / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / extrinsic apoptotic signaling pathway via death domain receptors / Activation of BAD and translocation to mitochondria / supramolecular fiber organization / positive regulation of intrinsic apoptotic signaling pathway / signal transduction in response to DNA damage / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / protein-containing complex assembly / neuron apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding / mitochondrion / membrane / cytosol
Similarity search - Function
Orthopoxvirus protein F1 / Poxvirus F1/C10 / Apoptosis regulator M11L like / BH3-interacting domain death agonist / BH3 interacting domain (BID) / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Bcl-2-like superfamily
Similarity search - Domain/homology
ACETATE ION / BH3-interacting domain death agonist / Apoptosis regulator OPG045
Similarity search - Component
Biological speciesVARIOLA VIRUS (smallpox virus)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKvansakul, M. / Colman, P.M.
CitationJournal: Cell Death Dis. / Year: 2015
Title: Variola Virus F1L is a Bcl-2-Like Protein that Unlike its Vaccinia Virus Counterpart Inhibits Apoptosis Independent of Bim.
Authors: Marshall, B. / Puthalakath, H. / Caria, S. / Chugh, S. / Doerflinger, M. / Colman, P.M. / Kvansakul, M.
History
DepositionFeb 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Atomic model / Derived calculations / Other
Revision 1.2Jul 29, 2015Group: Source and taxonomy
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOMOLOG OF VACCINIA VIRUS CDS F1L PUTATIVE
B: BH3-INTERACTING DOMAIN DEATH AGONIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5064
Polymers23,3552
Non-polymers1512
Water2,126118
1
A: HOMOLOG OF VACCINIA VIRUS CDS F1L PUTATIVE
B: BH3-INTERACTING DOMAIN DEATH AGONIST
hetero molecules

A: HOMOLOG OF VACCINIA VIRUS CDS F1L PUTATIVE
B: BH3-INTERACTING DOMAIN DEATH AGONIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0118
Polymers46,7094
Non-polymers3024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area11120 Å2
ΔGint-107.2 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.094, 112.318, 117.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-2024-

HOH

21A-2081-

HOH

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Components

#1: Protein HOMOLOG OF VACCINIA VIRUS CDS F1L PUTATIVE / VARIOLA VIRUS F1L / HOMOLOG OF VACCINIA VIRUS CDS F1L PUTATIVE SYNONYM VARIOLA VIRUS F1L


Mass: 19652.309 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VARIOLA VIRUS (smallpox virus) / Strain: BANGLADESH / Plasmid: PGEX-6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: Q85365
#2: Protein/peptide BH3-INTERACTING DOMAIN DEATH AGONIST / P22 BID / BID / P15 BID / P13 BID / P11 BID / P22 BID / BID / P15 BID / P13 BID / P11 BID / VARIOLA VIRUS F1L


Mass: 3702.206 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 79-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETHIC CDNA / Plasmid: PGEX-6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: P55957
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALSO KNOWN AS C5L

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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: 1.83 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.8 M SODIUM ACETATE AND 0.1 M HEPES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.975
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 17569 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 39
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.6 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1760)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D2M

4d2m


Resolution: 1.75→43.828 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 891 5.1 %
Rwork0.1668 --
obs0.1689 17534 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→43.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 10 118 1471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111378
X-RAY DIFFRACTIONf_angle_d1.151863
X-RAY DIFFRACTIONf_dihedral_angle_d13.848523
X-RAY DIFFRACTIONf_chiral_restr0.043217
X-RAY DIFFRACTIONf_plane_restr0.005238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.85960.28141480.22852732X-RAY DIFFRACTION100
1.8596-2.00320.22951380.18952766X-RAY DIFFRACTION100
2.0032-2.20480.20381590.14952718X-RAY DIFFRACTION100
2.2048-2.52380.18931390.1482767X-RAY DIFFRACTION100
2.5238-3.17960.18991560.17272786X-RAY DIFFRACTION100
3.1796-43.84190.21321510.16472874X-RAY DIFFRACTION99
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)
10.7989-0.2031.17841.073-0.75744.2178-0.00740.0087-0.2020.06830.10040.1570.1025-0.0899-0.08370.2390.0161-0.00370.18760.00740.2621-1.6954-19.55491.917
24.02760.18070.75798.258-4.42962.5826-0.2313-0.26290.30060.16650.28171.4615-0.6355-1.2442-0.37980.42620.05860.04090.70930.0630.6441-16.0885-15.813817.8709
33.7932-1.45091.52456.3061-4.76338.09410.0469-0.88460.24151.11020.53551.0822-1.1556-1.05060.38940.69230.21180.14130.22070.04110.3624-6.2375-2.648517.9072
42.133-0.11460.35433.0236-1.27934.6063-0.0808-0.1586-0.07760.34150.08960.0298-0.3594-0.0196-0.01550.2720.02350.02960.18250.01660.1885-0.4604-12.381114.7542
57.4208-2.67571.18778.0815-1.50152.91460.1918-0.73440.48960.69430.07820.4539-0.6339-0.9273-0.31820.52660.12980.1410.56140.09040.4698-9.6222-11.600925.5048
67.30592.3674-0.84318.8567-1.08540.89280.02-1.8804-0.02281.41180.0373-0.3062-0.51110.5991-0.22130.5845-0.0229-0.09510.70390.15560.41694.4978-23.359232.2497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 64 THROUGH 118 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 119 THROUGH 132 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 133 THROUGH 150 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 151 THROUGH 201 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 81 THROUGH 100 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 101 THROUGH 109 )

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