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- PDB-8sm5: Crystal Structure of BHRF1 from Epstein Barr Virus in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8sm5
TitleCrystal Structure of BHRF1 from Epstein Barr Virus in complex with BID BH3 peptide
Components
  • Apoptosis regulator BHRF1
  • BID BH3
KeywordsVIRAL PROTEIN / BHRF1 / BID peptide / complex / BH3 domain / apoptosis
Function / homology
Function and homology information


symbiont-mediated suppression of host apoptosis / suppression by virus of host autophagy / negative regulation of release of cytochrome c from mitochondria / host cell mitochondrion / host cell membrane / membrane
Similarity search - Function
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
Similarity search - Domain/homology
Apoptosis regulator BHRF1
Similarity search - Component
Biological speciesHuman herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61002612546 Å
AuthorsWyatt, S. / Sinha, S.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146232 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)RO3NS090939 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM122035 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P20 RR015566 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI078198 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM126207 United States
National Science Foundation (NSF, United States)MCB-1413525 United States
CitationJournal: Biochemistry / Year: 2023
Title: Epstein-Barr Virus Encoded BCL2, BHRF1, Downregulates Autophagy by Noncanonical Binding of BECN1.
Authors: Wyatt, S. / Glover, K. / Dasanna, S. / Lewison, M. / Gonzalez-Garcia, M. / Colbert, C.L. / Sinha, S.C.
History
DepositionApr 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator BHRF1
B: BID BH3
C: Apoptosis regulator BHRF1
D: BID BH3
E: Apoptosis regulator BHRF1
F: BID BH3
G: Apoptosis regulator BHRF1
H: BID BH3
I: Apoptosis regulator BHRF1
J: BID BH3


Theoretical massNumber of molelcules
Total (without water)99,72810
Polymers99,72810
Non-polymers00
Water66737
1
A: Apoptosis regulator BHRF1
B: BID BH3


Theoretical massNumber of molelcules
Total (without water)19,9462
Polymers19,9462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-15 kcal/mol
Surface area8730 Å2
MethodPISA
2
C: Apoptosis regulator BHRF1
D: BID BH3


Theoretical massNumber of molelcules
Total (without water)19,9462
Polymers19,9462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-14 kcal/mol
Surface area8620 Å2
MethodPISA
3
E: Apoptosis regulator BHRF1
F: BID BH3


Theoretical massNumber of molelcules
Total (without water)19,9462
Polymers19,9462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area8700 Å2
MethodPISA
4
G: Apoptosis regulator BHRF1
H: BID BH3


Theoretical massNumber of molelcules
Total (without water)19,9462
Polymers19,9462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-14 kcal/mol
Surface area8750 Å2
MethodPISA
5
I: Apoptosis regulator BHRF1
J: BID BH3


Theoretical massNumber of molelcules
Total (without water)19,9462
Polymers19,9462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-10 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.817, 186.817, 70.486
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
12
22
32
42
52

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAPHEPHEchain 'A'AA2 - 871 - 86
121METMETASPASPchain 'A'AA105 - 156104 - 155
211ALAALAPHEPHEchain 'C'CC2 - 871 - 86
221METMETASPASPchain 'C'CC105 - 156104 - 155
311ALAALAPHEPHEchain 'E'EE2 - 871 - 86
321METMETASPASPchain 'E'EE105 - 156104 - 155
411ALAALAPHEPHEchain 'G'GG2 - 871 - 86
421METMETASPASPchain 'G'GG105 - 156104 - 155
511ALAALAPHEPHEchain 'I'II2 - 871 - 86
521METMETASPASPchain 'I'II105 - 156104 - 155
112ILEILEMETMETchain 'B'BB82 - 972 - 17
212ILEILEMETMETchain 'D'DD82 - 972 - 17
312ILEILEMETMETchain 'F'FF82 - 972 - 17
412ILEILEMETMETchain 'H'HH82 - 972 - 17
512ILEILEMETMETchain 'J'JJ82 - 972 - 17

NCS ensembles :
ID
1
2

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Components

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


Mass: 17918.225 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: BHRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03182
#2: Protein/peptide
BID BH3


Mass: 2027.287 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 mM NaC2H3O2 pH 5.0, 1.6 mM HCOONa

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.61→161.79 Å / Num. obs: 42919 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 74.1969136487 Å2 / CC1/2: 0.998 / Net I/σ(I): 19.6
Reflection shellResolution: 2.61→2.71 Å / Num. unique obs: 4267 / CC1/2: 0.611

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61002612546→80.8941339294 Å / SU ML: 0.42999053392 / Cross valid method: FREE R-VALUE / σ(F): 1.34273956922 / Phase error: 27.1654184426
RfactorNum. reflection% reflection
Rfree0.259661322012 2164 5.04323102379 %
Rwork0.197565153955 40745 -
obs0.200666449516 42909 99.8301614629 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.394632263 Å2
Refinement stepCycle: LAST / Resolution: 2.61002612546→80.8941339294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6813 0 0 37 6850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008885805563686962
X-RAY DIFFRACTIONf_angle_d1.193312953829464
X-RAY DIFFRACTIONf_chiral_restr0.05241284294161071
X-RAY DIFFRACTIONf_plane_restr0.00688653049431214
X-RAY DIFFRACTIONf_dihedral_angle_d12.57171349492494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61002612546-2.70.4005515920171410.3415575917482680X-RAY DIFFRACTION99.9291533829
2.6707-2.73750.3573216899241460.2994681331582721X-RAY DIFFRACTION99.9651324965
2.7375-2.81160.3265499351881640.2808816168022676X-RAY DIFFRACTION99.9648011264
2.8116-2.89430.2994956233441470.2365350738782685X-RAY DIFFRACTION99.9647017296
2.8943-2.98770.2704547782191580.2200528772162667X-RAY DIFFRACTION100
2.9877-3.09450.2944709811961500.2133972051172726X-RAY DIFFRACTION100
3.0945-3.21840.3056630456411320.2152523095952726X-RAY DIFFRACTION100
3.2184-3.36490.2693608792551390.2165437324612698X-RAY DIFFRACTION100
3.3649-3.54230.2626600536931340.2032451616872727X-RAY DIFFRACTION100
3.5423-3.76420.2699514914131470.1977560763452732X-RAY DIFFRACTION100
3.7642-4.05490.2814101040181340.1943169807712704X-RAY DIFFRACTION100
4.0549-4.46290.2282049838141360.1766065465952748X-RAY DIFFRACTION100
4.4629-5.10860.2245691769261480.1784941431552727X-RAY DIFFRACTION100
5.1086-6.43590.2866486738961470.2179809557832765X-RAY DIFFRACTION100
6.4359-80.89413392940.2232088621341410.1660401090062763X-RAY DIFFRACTION97.7119784657
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)
15.09815259821-0.2936095735551.462217409435.988544692510.2394680454333.308527955090.06175817296250.12398563119-0.557136078056-0.04120200401130.1502740590130.0484908354380.100009428192-0.0515707925106-0.1794604902730.5970710294520.02385947172360.06739048482130.434560363543-0.04403326318880.35004236387590.9441741774-30.0563143873-9.75667829201
22.810151153240.176746024280.2283057858433.59174515631-0.317925817794.49835506555-0.3035967898990.11209930190.276140846179-0.2042564120080.532477956280.362024157667-1.02242906103-0.000416596125103-0.2329285880941.22485250817-0.1152207918320.0517581451910.552614622950.05001371556830.27894611925487.02684905182.08747062325-20.3037440761
35.8861612165-0.494425277574-0.844454218096.847036833372.584567243614.147122503150.0030268904535-0.2664338707920.45642803324-0.0678538632854-0.3874799117960.956477852723-0.149033977707-0.4177045166270.3780443064170.44721901285-0.0393695358948-0.04152697283160.509913972311-0.1103205282060.66820351012960.8932840284-40.7403829321-18.1536692883
48.76252205237-4.226525788271.058706839046.969320742420.8192001995886.205504992870.9155814214161.07344323587-1.88459481122-0.0129581837863-0.2681627446010.8169751776680.2083424710160.0551122734238-0.3835824286621.48816008396-0.1188651918030.04325430104770.923386897181-0.06297772055031.1464804075269.7726093112-28.248999035-60.7646559252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain C
3X-RAY DIFFRACTION3Chain E
4X-RAY DIFFRACTION4Chain H

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