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- PDB-2xpx: Crystal structure of BHRF1:Bak BH3 complex -

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Basic information

Entry
Database: PDB / ID: 2xpx
TitleCrystal structure of BHRF1:Bak BH3 complex
Components
  • APOPTOSIS REGULATOR BHRF1
  • BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
KeywordsAPOPTOSIS / MEMBRANE PROTEIN
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / symbiont-mediated perturbation of host apoptosis ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / suppression by virus of host autophagy / 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 / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / 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 / BH domain binding / porin activity / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / vagina development / B cell homeostasis / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / host cell membrane / host cell mitochondrion / blood vessel remodeling / cellular response to unfolded protein / 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 / epithelial cell proliferation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / establishment of localization in cell / response to gamma radiation / 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 / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / protein-containing complex binding / apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Apoptosis regulator BHRF1 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 4 (Epstein-Barr virus)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKvansakul, M. / Huang, D.C.S. / Colman, P.M.
CitationJournal: Plos Pathog. / Year: 2010
Title: Structural Basis for Apoptosis Inhibition by Epstein-Barr Virus Bhrf1.
Authors: Kvansakul, M. / Wei, A.H. / Fletcher, J.I. / Willis, S.N. / Chen, L. / Roberts, A.W. / Huang, D.C.S. / Colman, P.M.
History
DepositionAug 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Version format compliance
Revision 1.2Dec 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_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: APOPTOSIS REGULATOR BHRF1
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1038
Polymers22,7312
Non-polymers3726
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-5.9 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.387, 62.387, 93.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein APOPTOSIS REGULATOR BHRF1 / BHRF1 / EARLY ANTIGEN PROTEIN R / EA-R / NUCLEAR ANTIGEN


Mass: 19848.367 Da / Num. of mol.: 1 / Fragment: BCL-2, RESIDUES 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
Plasmid: PDUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: P03182
#2: Protein/peptide BCL-2 HOMOLOGOUS ANTAGONIST/KILLER / BAK / APOPTOSIS REGULATOR BAK / BCL-2-LIKE PROTEIN 7 / BCL2-L-7


Mass: 2882.151 Da / Num. of mol.: 1 / Fragment: RESIDUES 67-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: Q16611
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 4.4 / Details: 1.6 M NANO3, 50 MM MALIC ACID PH 4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 12945 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.9
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6Q

2v6q


Resolution: 2.05→19.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.364 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21696 668 4.9 %RANDOM
Rwork0.18352 ---
obs0.18505 12943 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.774 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 24 73 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211457
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9411972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6465179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0122.20668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68215236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7591515
X-RAY DIFFRACTIONr_chiral_restr0.1380.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021098
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1381.5891
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94821417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0743566
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5484.5552
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: 2.053→2.106 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 56 -
Rwork0.248 889 -
obs--94.41 %
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)
11.3537-0.26670.02062.27970.83982.6404-0.00890.02090.00960.04270.1326-0.1468-0.1170.1694-0.12370.17510.0190.00160.184-0.02450.1773-31.499810.6644-20.8262
214.91084.947117.60678.37387.626125.016-0.93820.28011.3377-1.0029-0.0777-0.0629-1.53680.2841.01590.40490.00230.06530.01830.02860.2372-32.907226.1778-22.156
32.01520.63790.36092.25060.5562.4111-0.0872-0.0872-0.04050.10070.1273-0.0991-0.06660.1512-0.040.41160.04180.03460.4376-0.02240.4279-32.495610.3165-19.951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 157
2X-RAY DIFFRACTION2B69 - 91
3X-RAY DIFFRACTION3A1158 - 1163
4X-RAY DIFFRACTION3A2001 - 2065
5X-RAY DIFFRACTION3B2001 - 2008

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