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- PDB-4d2m: Vaccinia Virus F1L bound to Bim BH3 -

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Basic information

Entry
Database: PDB / ID: 4d2m
TitleVaccinia Virus F1L bound to Bim BH3
Components
  • BCL-2-LIKE PROTEIN 11
  • PROTEIN F1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / host cell mitochondrial outer membrane / RUNX3 regulates BCL2L11 (BIM) transcription / : / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / host cell mitochondrial outer membrane / RUNX3 regulates BCL2L11 (BIM) transcription / : / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / tube formation / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / regulation of organ growth / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / B cell homeostasis / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / spleen development / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 Signaling / response to endoplasmic reticulum stress / post-embryonic development / cell-matrix adhesion / thymus development / kidney development / positive regulation of protein-containing complex assembly / : / male gonad development / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / microtubule binding / spermatogenesis / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / molecular adaptor activity / positive regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / membrane / cytosol
Similarity search - Function
Orthopoxvirus protein F1 / Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x ...Orthopoxvirus protein F1 / Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 11 / Apoptosis regulator OPG045
Similarity search - Component
Biological speciesVACCINIA VIRUS ANKARA
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Jun 18, 2014Group: Atomic model
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: PROTEIN F1
B: BCL-2-LIKE PROTEIN 11
C: PROTEIN F1
D: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9429
Polymers49,6824
Non-polymers2605
Water2,216123
1
A: PROTEIN F1
B: BCL-2-LIKE PROTEIN 11
C: PROTEIN F1
D: BCL-2-LIKE PROTEIN 11
hetero molecules

A: PROTEIN F1
B: BCL-2-LIKE PROTEIN 11
C: PROTEIN F1
D: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,88418
Polymers99,3648
Non-polymers52010
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area24260 Å2
ΔGint-285.7 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.503, 56.503, 232.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1189-

CL

21C-1188-

CL

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Components

#1: Protein PROTEIN F1


Mass: 21566.379 Da / Num. of mol.: 2 / Fragment: RESIDUES 18-186 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS ANKARA / 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-LIKE PROTEIN 11 / BCL2-L-11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH


Mass: 3274.691 Da / Num. of mol.: 2 / Fragment: RESIDUES 141-166
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: O43521
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 6.2
Details: 0.2M KCL, 15 % PEG400, 1.44 % MPD AND 0.1M AMMONIUM CITRATE PH 6.2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→46.54 Å / Num. obs: 23011 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 35.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 12 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

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

2vty


Resolution: 2.1→37.788 Å / SU ML: 0.24 / σ(F): 1.9 / Phase error: 26.06 / Stereochemistry target values: ML
Details: RESIDUE C156 HARBOURS A COVALENT MODIFICATION THAT WAS INTERPRETED AS BME.
RfactorNum. reflection% reflection
Rfree0.255 1181 5.1 %
Rwork0.2148 --
obs0.2168 23008 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→37.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 12 123 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032674
X-RAY DIFFRACTIONf_angle_d0.6263607
X-RAY DIFFRACTIONf_dihedral_angle_d12.8751007
X-RAY DIFFRACTIONf_chiral_restr0.026404
X-RAY DIFFRACTIONf_plane_restr0.002453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19560.32291460.24652618X-RAY DIFFRACTION100
2.1956-2.31130.28641560.2392641X-RAY DIFFRACTION100
2.3113-2.45610.2731370.22132727X-RAY DIFFRACTION100
2.4561-2.64570.26861620.2252654X-RAY DIFFRACTION100
2.6457-2.91190.22641560.2082702X-RAY DIFFRACTION100
2.9119-3.3330.2661360.22042754X-RAY DIFFRACTION100
3.333-4.19840.24671440.1992772X-RAY DIFFRACTION100
4.1984-37.79360.2411440.2142959X-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)
15.679-0.8081-0.39451.87980.49382.0212-0.0104-0.150.2064-0.4171-0.08810.26420.0251-0.24530.17080.4404-0.0665-0.09460.26890.00030.24555.271615.6293-16.6723
22.3834-0.33060.33462.8322-0.11962.91290.05390.0916-0.3169-0.2235-0.0566-0.08860.28280.01360.02920.4086-0.03250.07470.2404-0.03520.261921.5845-0.1327-13.2535
34.2844-0.37932.50091.6320.08233.60980.35180.2276-1.4053-0.3263-0.5054-0.76021.41250.53260.63590.79930.04410.03440.29050.03370.785423.8839-12.1752-12.9796
45.1036-1.1320.23361.6172-0.57691.9379-0.0288-0.72840.4486-0.0507-0.1105-0.0615-0.54120.13190.12470.5705-0.10560.0550.3242-0.0450.301320.965310.8431-16.7805
52.2848-0.6808-0.51752.8043-0.0532.59790.02890.08760.3242-0.2473-0.00090.011-0.2823-0.0155-0.04170.4316-0.0491-0.03910.29670.01320.31614.760926.6355-13.127
62.3265-0.6401-0.41191.8178-0.85663.07450.1760.22950.8271-0.2804-0.4853-0.1974-0.9456-0.38550.29120.90290.1218-0.02220.34330.00090.70752.875638.8158-12.4239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 51 THROUGH 81 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 82 THROUGH 186 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 53 THROUGH 74 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 51 THROUGH 81 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 82 THROUGH 186 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 53 THROUGH 73 )

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