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Basic information

Entry
Database: PDB / ID: 4oyd
TitleCrystal structure of a computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein
Components
  • Apoptosis regulator BHRF1
  • Computationally designed Inhibitor
KeywordsViral Protein/Inhibitor / Inhibitor / complex / apoptosis / Viral Protein-Inhibitor complex
Function / homology
Function and homology information


suppression by virus of host autophagy / host cell mitochondrion / host cell membrane / regulation of apoptotic process / membrane
Similarity search - Function
Ribosome-recycling factor / Topoisomerase I; Chain A, domain 4 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. ...Ribosome-recycling factor / Topoisomerase I; Chain A, domain 4 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / 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 BHRF1
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsShen, B. / Procko, E. / Baker, D. / Stoddard, B.
CitationJournal: Cell / Year: 2014
Title: A computationally designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells.
Authors: Procko, E. / Berguig, G.Y. / Shen, B.W. / Song, Y. / Frayo, S. / Convertine, A.J. / Margineantu, D. / Booth, G. / Correia, B.E. / Cheng, Y. / Schief, W.R. / Hockenbery, D.M. / Press, O.W. / ...Authors: Procko, E. / Berguig, G.Y. / Shen, B.W. / Song, Y. / Frayo, S. / Convertine, A.J. / Margineantu, D. / Booth, G. / Correia, B.E. / Cheng, Y. / Schief, W.R. / Hockenbery, D.M. / Press, O.W. / Stoddard, B.L. / Stayton, P.S. / Baker, D.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_entity_src_syn ...entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / pdbx_validate_polymer_linkage
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_polymer_linkage.label_alt_id_1
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator BHRF1
B: Computationally designed Inhibitor
C: Apoptosis regulator BHRF1
D: Computationally designed Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0595
Polymers63,9974
Non-polymers621
Water2,972165
1
A: Apoptosis regulator BHRF1
B: Computationally designed Inhibitor


Theoretical massNumber of molelcules
Total (without water)31,9992
Polymers31,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-8 kcal/mol
Surface area14180 Å2
MethodPISA
2
C: Apoptosis regulator BHRF1
D: Computationally designed Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0613
Polymers31,9992
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-7 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.103, 113.869, 55.670
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA1 - 1561 - 156
21SERSERASPASPCC1 - 1561 - 156
12ALAALAGLYGLYBB1 - 1171 - 117
22ALAALAGLYGLYDD1 - 1171 - 117

NCS ensembles :
ID
1
2
Detailsgelfiltration

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Components

#1: Protein Apoptosis regulator BHRF1 / Early antigen protein R / EA-R / Nuclear antigen


Mass: 18118.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Strain: AG876 / Gene: BHRF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C6Z1
#2: Protein Computationally designed Inhibitor


Mass: 13880.071 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 52.33 % / Description: physically twinned.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG8000, magnesium chloride, TrisHCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→39.8 Å / Num. obs: 46840 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rsym value: 0.099 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.47 / % possible all: 80.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 1.8→39.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.321 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17845 2487 5 %RANDOM
Rwork0.14502 ---
obs0.14676 46840 82.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.168 Å2
Baniso -1Baniso -2Baniso -3
1--8.77 Å20 Å2-3.76 Å2
2--8.02 Å20 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.8→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 4 165 4642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194815
X-RAY DIFFRACTIONr_bond_other_d0.0050.024670
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9686518
X-RAY DIFFRACTIONr_angle_other_deg1.34310752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26423.548248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92415931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3351552
X-RAY DIFFRACTIONr_chiral_restr0.1230.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025508
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021128
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6361.5782318
X-RAY DIFFRACTIONr_mcbond_other1.6351.5782317
X-RAY DIFFRACTIONr_mcangle_it2.5022.3452928
X-RAY DIFFRACTIONr_mcangle_other2.5022.3462929
X-RAY DIFFRACTIONr_scbond_it2.4411.9632497
X-RAY DIFFRACTIONr_scbond_other2.4381.9632497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9132.8173586
X-RAY DIFFRACTIONr_long_range_B_refined5.60412.9635753
X-RAY DIFFRACTIONr_long_range_B_other5.60412.9645754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A82760.16
12C82760.16
21B73540.09
22D73540.09
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 46 -
Rwork0.207 876 -
obs--20.94 %
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)
12.3642-0.0065-0.19161.31620.07511.985-0.0216-0.044-0.1114-0.02550.0118-0.10090.12530.13630.00980.0090.00460.00410.0621-0.00790.014810.328323.713-35.5962
22.87871.23960.20983.01090.29571.84810.0496-0.07220.38520.1084-0.02450.073-0.2790.0799-0.0250.06760.02250.02310.08970.01150.0669-4.170537.6208-28.5331
32.50880.1246-0.01821.6504-0.01581.7705-0.0334-0.00040.0616-0.06350.02030.1151-0.0692-0.12990.01310.00660.0088-0.0050.02890.00310.0097-23.050828.8432-7.7564
42.41362.1685-0.7043.42-0.69750.94250.0311-0.0192-0.11720.1028-0.0199-0.07860.09120.0539-0.01120.02830.025-0.0060.0399-0.00150.0102-8.713815.2771-0.5725
50.15660.0096-0.14930.0587-0.04610.3740.0198-0.0187-0.01360.0033-0.00780.01530.0041-0.0097-0.01190.0841-0.00120.00830.11710.00760.0991-10.145423.7188-13.6685
612.609623.6357-3.3933120.592-62.485442.20390.033-0.1344-0.01370.9805-0.6132-0.8066-0.68650.30230.58030.0421-0.002-0.0310.087-0.00930.0775-31.3864-5.8978.4614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION2B1 - 117
3X-RAY DIFFRACTION3C1 - 158
4X-RAY DIFFRACTION4D1 - 117
5X-RAY DIFFRACTION5A201 - 236
6X-RAY DIFFRACTION5B201 - 223
7X-RAY DIFFRACTION5C201 - 250
8X-RAY DIFFRACTION5D301 - 344
9X-RAY DIFFRACTION6D201

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