- PDB-4uf1: Deerpox virus DPV022 in complex with Bak BH3 -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4uf1
Title
Deerpox virus DPV022 in complex with Bak BH3
Components
Antiapoptotic membrane protein
Bcl-2 homologous antagonist/killer
Keywords
VIRAL PROTEIN / DEERPOX VIRUS / APOPTOSIS / BCL-2 / BAK BH3
Function / homology
Function and homology information
Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / 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 / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / 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 / positive regulation of calcium ion transport into cytosol / porin activity / pore complex / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / host cell mitochondrion / host cell membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / 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 / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / 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 / regulation of apoptotic process / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / metal ion binding / cytosol Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / 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. ...Poxvirus F1/C10 / Apoptosis regulator M11L like / 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 (B-Cell lymphoma); contains BH1, BH2 regions / 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
Journal: Acta Crystallogr D Biol Crystallogr / Year: 2015 Title: Structural basis of Deerpox virus-mediated inhibition of apoptosis. Authors: Denis R Burton / Sofia Caria / Bevan Marshall / Michele Barry / Marc Kvansakul / Abstract: Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use ...Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that the Deerpox virus inhibitor of apoptosis, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteins via two conserved ligand-binding grooves found on opposite sides of the dimer. Structures of DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of DPV022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.
History
Deposition
Dec 23, 2014
Deposition site: PDBE / Processing site: PDBE
Revision 1.0
Aug 5, 2015
Provider: repository / Type: Initial release
Revision 1.1
Aug 12, 2015
Group: Database references
Revision 1.2
Aug 19, 2015
Group: Database references
Revision 2.0
Oct 23, 2019
Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2013 / Details: SILICON MIRRORS (ADAPTIVE AND U-BENT)
Radiation
Monochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9537 Å / Relative weight: 1
Reflection
Resolution: 2.3→41.71 Å / Num. obs: 9129 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9
Reflection shell
Resolution: 2.3→2.39 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.1 / % possible all: 99
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
iMOSFLM
datareduction
Aimless
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: DPV022_BIM Resolution: 2.3→41.707 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 22.37 / Stereochemistry target values: ML Details: RESIDUES FROM 1 AND 2 AND FROM 138 TO 155 ARE MISSING IN DPV022. IN BAK,THE RESIDUES 67 AND 68 AS WELL AS 91 AND 92
Rfactor
Num. reflection
% reflection
Rfree
0.2059
446
4.9 %
Rwork
0.1782
-
-
obs
0.1796
9109
96.99 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 48.7 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→41.707 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1272
0
5
42
1319
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
1289
X-RAY DIFFRACTION
f_angle_d
0.732
1731
X-RAY DIFFRACTION
f_dihedral_angle_d
15.135
496
X-RAY DIFFRACTION
f_chiral_restr
0.032
200
X-RAY DIFFRACTION
f_plane_restr
0.002
218
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3001-2.6329
0.2488
153
0.2057
2851
X-RAY DIFFRACTION
98
2.6329-3.3169
0.2418
140
0.1962
2853
X-RAY DIFFRACTION
97
3.3169-41.714
0.1792
153
0.1619
2959
X-RAY DIFFRACTION
96
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
2.6281
0.0095
-0.2805
1.3058
-0.6035
2.1623
0.1698
0.1201
-0.0881
0.073
-0.0762
0.0779
0.2045
0.1955
-0.0256
0.2954
0.0669
0.0136
0.2207
-0.0324
0.2097
-12.063
-18.75
8.3895
2
4.9616
-2.8981
-1.7708
4.4305
1.653
4.9795
0.0627
-0.3638
0.3797
-0.2335
0.1124
-0.1183
-0.308
0.5746
0.0623
0.1948
-0.0243
0.0056
0.2306
-0.0075
0.2017
-14.8096
-3.5885
-11.2717
3
2.5309
-0.8648
0.5259
2.6683
-0.0234
3.9467
-0.0795
-0.0726
-0.1236
0.2657
0.0744
0.6216
0.0488
-0.2603
-0.036
0.2311
0.0507
0.03
0.2625
-0.0025
0.3712
-29.6476
-7.5456
-6.4159
4
5.2604
0.7429
0.1807
4.5652
-1.4622
5.6576
0.3773
0.4045
0.2132
-0.1628
-0.7232
0.354
-0.9461
-0.6826
0.0359
0.4887
0.1692
-0.0415
0.4041
-0.0547
0.4542
-34.0207
3.5549
-12.4463
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN 'A' AND (RESID3THROUGH30 )
2
X-RAY DIFFRACTION
2
CHAIN 'A' AND (RESID31THROUGH52 )
3
X-RAY DIFFRACTION
3
CHAIN 'A' AND (RESID53THROUGH137 )
4
X-RAY DIFFRACTION
4
CHAIN 'B' AND (RESID69THROUGH90 )
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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