[English] 日本語
Yorodumi
- PDB-7p33: Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p33
TitleEpstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide
Components
  • Apoptosis regulator BHRF1
  • BH3-interacting domain death agonist p15
KeywordsAPOPTOSIS / Gamma herpes virus / Epstein-Barr virus / BHRF-1 / Bcl-2
Function / homology
Function and homology information


cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / symbiont-mediated suppression of host apoptosis / positive regulation of fibroblast apoptotic process / suppression by virus of host autophagy / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / symbiont-mediated suppression of host apoptosis / positive regulation of fibroblast apoptotic process / suppression by virus of host autophagy / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to mitochondrion / regulation of epithelial cell proliferation / establishment of protein localization to membrane / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / regulation of T cell proliferation / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / regulation of G1/S transition of mitotic cell cycle / apoptotic mitochondrial changes / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / mitochondrial ATP synthesis coupled electron transport / host cell mitochondrion / extrinsic apoptotic signaling pathway via death domain receptors / host cell membrane / Activation of BAD and translocation to mitochondria / signal transduction in response to DNA damage / supramolecular fiber organization / positive regulation of intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / protein-containing complex assembly / neuron apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding / mitochondrion / membrane / cytosol
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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
PHOSPHATE ION / Apoptosis regulator BHRF1 / BH3-interacting domain death agonist
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78542723478 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Viruses / Year: 2022
Title: Crystal Structures of Epstein-Barr Virus Bcl-2 Homolog BHRF1 Bound to Bid and Puma BH3 Motif Peptides.
Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apoptosis regulator BHRF1
B: Apoptosis regulator BHRF1
C: Apoptosis regulator BHRF1
D: Apoptosis regulator BHRF1
E: Apoptosis regulator BHRF1
G: BH3-interacting domain death agonist p15
H: BH3-interacting domain death agonist p15
F: BH3-interacting domain death agonist p15
I: BH3-interacting domain death agonist p15
J: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,86412
Polymers117,70710
Non-polymers1572
Water1,11762
1
A: Apoptosis regulator BHRF1
G: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)23,5412
Polymers23,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-16 kcal/mol
Surface area10090 Å2
MethodPISA
2
B: Apoptosis regulator BHRF1
F: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)23,5412
Polymers23,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area8960 Å2
MethodPISA
3
C: Apoptosis regulator BHRF1
H: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6043
Polymers23,5412
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-13 kcal/mol
Surface area10190 Å2
MethodPISA
4
D: Apoptosis regulator BHRF1
I: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6363
Polymers23,5412
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-17 kcal/mol
Surface area9550 Å2
MethodPISA
5
E: Apoptosis regulator BHRF1
J: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)23,5412
Polymers23,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-14 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.208, 94.208, 455.582
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
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,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

-
Components

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


Mass: 19848.367 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: BHRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03182
#2: Protein/peptide
BH3-interacting domain death agonist p15 / p15 BID


Mass: 3693.111 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.68 % / Description: thick hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4M Ammonium phosphate mono basic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.785→46.8542271629 Å / Num. obs: 28893 / % possible obs: 92.17 % / Redundancy: 11.9 % / Biso Wilson estimate: 59.5883072532 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.4
Reflection shellResolution: 2.785→2.94 Å / Rmerge(I) obs: 1.207 / Num. unique obs: 4267 / CC1/2: 0.586

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless7.1.007data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XPX

2xpx


Resolution: 2.78542723478→46.8542271629 Å / SU ML: 0.437300470854 / Cross valid method: FREE R-VALUE / σ(F): 1.3497953026 / Phase error: 28.0524443425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274075422541 1396 4.83563684229 %
Rwork0.22970835287 27473 -
obs0.231906605748 28869 92.1978794073 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.4775184542 Å2
Refinement stepCycle: LAST / Resolution: 2.78542723478→46.8542271629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 9 62 7263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002014675076697353
X-RAY DIFFRACTIONf_angle_d0.3966130372769978
X-RAY DIFFRACTIONf_chiral_restr0.03181316873081123
X-RAY DIFFRACTIONf_plane_restr0.002118132500411277
X-RAY DIFFRACTIONf_dihedral_angle_d18.35679578434339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78542723478-2.8850.3795809090031410.3105538823822731X-RAY DIFFRACTION94.8794185662
2.885-3.00050.3302331044051430.2947792526842854X-RAY DIFFRACTION98.1335952849
3.0005-3.1370.3723836307291520.2666284189862851X-RAY DIFFRACTION98.0091383812
3.137-3.30230.3092669774251240.2470719983442841X-RAY DIFFRACTION97.8225008248
3.3023-3.50920.2716833110111110.2531873211692292X-RAY DIFFRACTION77.5161290323
3.5092-3.780.2766520255151120.2355467408452443X-RAY DIFFRACTION82.4725629438
3.78-4.16020.2806255163871320.2022041435272510X-RAY DIFFRACTION85.2533075186
4.1602-4.76170.2119344768981710.1791278731842886X-RAY DIFFRACTION96.8324358568
4.7617-5.99720.2440642991791560.2116721792162937X-RAY DIFFRACTION96.2651727358

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more