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- PDB-2v6q: Crystal Structure of a BHRF-1 : Bim BH3 complex -

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Basic information

Entry
Database: PDB / ID: 2v6q
TitleCrystal Structure of a BHRF-1 : Bim BH3 complex
Components
  • BCL-2-LIKE PROTEIN 11
  • BHRF1 PROTEIN
KeywordsAPOPTOSIS / ALTERNATIVE SPLICING / BCL-2 / MEMBRANE
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 / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / symbiont-mediated suppression of host apoptosis / positive regulation of fibroblast apoptotic process ...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 / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / symbiont-mediated suppression of host apoptosis / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / suppression by virus of host autophagy / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / tube formation / 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 / negative regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / host cell mitochondrion / host cell membrane / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / cell-matrix adhesion / post-embryonic development / thymus development / kidney development / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / spermatogenesis / microtubule binding / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / membrane => GO:0016020 / 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. / Bcl-2 family ...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. / Bcl-2 family / 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
BROMIDE ION / Bcl-2-like protein 11 / Apoptosis regulator BHRF1 / Apoptosis regulator BHRF1
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 4 (Epstein-Barr virus)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 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
DepositionJul 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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 / software / 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 / _software.name / _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: BHRF1 PROTEIN
B: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5237
Polymers23,1232
Non-polymers4005
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-16.3 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.736, 62.736, 92.523
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 BHRF1 PROTEIN / BHRF1 / EA-R / NUCLEAR ANTIGEN / BHRF-1 / EARLY ANTIGEN PROTEIN R


Mass: 19848.367 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-160 / Source method: isolated from a natural source / Source: (natural) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) / Strain: GD1 / References: UniProt: P03182, UniProt: P0C736*PLUS
#2: Protein/peptide BCL-2-LIKE PROTEIN 11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH / BCL2-L-11 / BCL2-LIKE 11 TRANSCRIPT VARIANT 9 / BIM


Mass: 3274.691 Da / Num. of mol.: 1 / Fragment: RESIDUES 141-166 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O43521
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2

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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 4.0, 1.7 M NABR, 0.1 M GUANIDINE HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.5479
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5479 Å / Relative weight: 1
ReflectionResolution: 2.7→35.22 Å / Num. obs: 6089 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 27.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.7→35.22 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.886 / SU B: 29.204 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 296 4.9 %RANDOM
Rwork0.206 ---
obs0.208 5792 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 5 27 1473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211476
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9332008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0645177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1222.83874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36715238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5321514
X-RAY DIFFRACTIONr_chiral_restr0.110.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.2749
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21008
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.861.5889
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58921432
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7413587
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8854.5576
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 24 -
Rwork0.294 375 -
obs--92.58 %
Refinement TLS params.Method: refined / Origin x: 32.044 Å / Origin y: 12.7015 Å / Origin z: 5.7113 Å
111213212223313233
T0.1007 Å2-0.0329 Å2-0.0058 Å2-0.0823 Å20.0055 Å2--0.0557 Å2
L0.8183 °20.0787 °2-0.28 °2-1.3949 °2-0.4793 °2--1.3121 °2
S-0.0281 Å °-0.0098 Å °0.012 Å °-0.0523 Å °0.0722 Å °0.0263 Å °-0.0929 Å °-0.0302 Å °-0.0441 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION1A1157 - 1160
3X-RAY DIFFRACTION1A2002 - 2026
4X-RAY DIFFRACTION1B2001
5X-RAY DIFFRACTION1B51 - 72

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