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- PDB-2wh6: Crystal structure of anti-apoptotic BHRF1 in complex with the Bim... -

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Basic information

Entry
Database: PDB / ID: 2wh6
TitleCrystal structure of anti-apoptotic BHRF1 in complex with the Bim BH3 domain
Components
  • BCL-2-LIKE PROTEIN 11
  • EARLY ANTIGEN PROTEIN R
KeywordsAPOPTOSIS / MITOCHONDRION / EARLY PROTEIN / TRANSMEMBRANE / VIRAL PROTEIN
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / symbiont-mediated suppression of host apoptosis / ear development / symbiont-mediated suppression of host autophagy / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mammary gland development / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / myeloid cell homeostasis / NRAGE signals death through JNK / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / B cell homeostasis / host cell membrane / host cell mitochondrion / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / FLT3 Signaling / endomembrane system / response to endoplasmic reticulum stress / thymus development / cell-matrix adhesion / post-embryonic development / kidney development / positive regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / microtubule binding / regulation of apoptotic process / spermatogenesis / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / membrane / cytosol
Similarity search - Function
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 / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. ...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 / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / 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
BROMIDE ION / Bcl-2-like protein 11 / Apoptosis regulator BHRF1 / Apoptosis regulator BHRF1
Similarity search - Component
Biological speciesEpstein-barr virus strain ag876
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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. / Colman, P.M.
History
DepositionMay 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 28, 2018Group: Advisory / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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Assembly

Deposited unit
A: EARLY ANTIGEN PROTEIN R
B: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,02613
Polymers23,1232
Non-polymers90311
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-17.5 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.747, 62.747, 92.383
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 EARLY ANTIGEN PROTEIN R / NUCLEAR ANTIGEN / EA-R / BHRF1


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.) Epstein-barr virus strain ag876 / Plasmid: PDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03182, UniProt: P0C6Z1*PLUS
#2: Protein/peptide BCL-2-LIKE PROTEIN 11 / BCL2-L-11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH / BIM


Mass: 3274.691 Da / Num. of mol.: 1 / Fragment: BH3, RESIDUES 51-72 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O43521
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 4 / Details: 0.1 M MALIC ACID PH 4 1.25 M NABR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.987
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 32170 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 40
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6Q

2v6q


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.875 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1705 5 %RANDOM
Rwork0.198 ---
obs0.199 32170 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 21 115 1593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211504
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9422046
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6785183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.78923.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40215246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2971514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021145
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.2810
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21040
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2620.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.432918
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37131455
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4045670
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6686588
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 104
Rwork0.297 2169
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)
10.30530.342-0.28751.0312-0.5981.5152-0.05550.0472-0.0333-0.05070.0960.0569-0.1177-0.0378-0.0404-0.0182-0.0351-0.0121-0.06020.0172-0.0487-31.286310.82814.9905
27.59780.64732.5023.27181.27133.33410.0839-0.27230.5385-0.4480.23270.005-0.49160.3781-0.31660.1921-0.09040.1041-0.1638-0.0042-0.0635-27.169224.92969.2571
31.53280.2994-0.33451.2257-0.62952.46350.0016-0.03510.02290.05830.0496-0.0564-0.1638-0.0246-0.05120.0402-0.0183-0.00060.02840.00050.0625-30.605112.57915.2648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION2B51 - 76
3X-RAY DIFFRACTION3A2001 - 2099
4X-RAY DIFFRACTION3B2001 - 2016
5X-RAY DIFFRACTION3A1159 - 1167
6X-RAY DIFFRACTION3A1168 - 1169

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