- EMDB-0208: OBP chaperonin in the ATPgammaS-bound state -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-0208
Title
OBP chaperonin in the ATPgammaS-bound state
Map data
A symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the ATPgammaS-bound state.
Sample
Complex: OBP chaperonin in complex with ATPgammaS
Biological species
Pseudomonas phage OBP (virus)
Method
single particle reconstruction / cryo EM / Resolution: 5.0 Å
Journal: J Struct Biol / Year: 2020 Title: Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin. Authors: Tatiana B Stanishneva-Konovalova / Pavel I Semenyuk / Lidia P Kurochkina / Evgeny B Pichkur / Alexander L Vasilyev / Mikhail V Kovalchuk / Mikhail P Kirpichnikov / Olga S Sokolova / Abstract: Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They ...Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins. Here, we solved the symmetry-free cryo-EM structures of a single-ring chaperonin encoded by the gene 246 of bacteriophage OBP Pseudomonas fluorescens, in the nucleotide-free, ATPγS-, and ADP-bound states, with resolutions of 4.3 Å, 5.0 Å, and 6 Å, respectively. The structure of OBP chaperonin reveals a unique subunit arrangement, with three pairs of subunits and one unpaired subunit. Each pair combines subunits in two possible conformations, differing in nucleotide-binding affinity. The binding of nucleotides results in the increase of subunits' conformational variability. Due to its unique structural and functional features, OBP chaperonin can represent a new group.
History
Deposition
Aug 20, 2018
-
Header (metadata) release
Oct 24, 2018
-
Map release
Aug 28, 2019
-
Update
Sep 9, 2020
-
Current status
Sep 9, 2020
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_0208.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
A symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the ATPgammaS-bound state.
Voxel size
X=Y=Z: 1.72 Å
Density
Contour Level
By AUTHOR: 0.226 / Movie #1: 0.226
Minimum - Maximum
-0.32981038 - 0.72862643
Average (Standard dev.)
0.00005425383 (±0.046707384)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
132
132
132
Spacing
132
132
132
Cell
A=B=C: 227.04001 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.72
1.72
1.72
M x/y/z
132
132
132
origin x/y/z
0.000
0.000
0.000
length x/y/z
227.040
227.040
227.040
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
132
132
132
D min/max/mean
-0.330
0.729
0.000
-
Supplemental data
-
Sample components
-
Entire : OBP chaperonin in complex with ATPgammaS
Entire
Name: OBP chaperonin in complex with ATPgammaS
Components
Complex: OBP chaperonin in complex with ATPgammaS
-
Supramolecule #1: OBP chaperonin in complex with ATPgammaS
Supramolecule
Name: OBP chaperonin in complex with ATPgammaS / type: complex / ID: 1 / Parent: 0
Source (natural)
Organism: Pseudomonas phage OBP (virus)
Recombinant expression
Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight
Experimental: 420 KDa
-
Experimental details
-
Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Concentration
2.5 mg/mL
Buffer
pH: 7.5
Vitrification
Cryogen name: ETHANE
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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