- EMDB-0204: OBP chaperonin in the nucleotide-free state -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-0204
Title
OBP chaperonin in the nucleotide-free 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 nucleotide-free state.
Sample
Complex: OBP chaperonin in the nucleotide-free state
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 17, 2018
-
Header (metadata) release
Oct 31, 2018
-
Map release
Aug 28, 2019
-
Update
May 15, 2024
-
Current status
May 15, 2024
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_0204.map.gz / Format: CCP4 / Size: 64 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 nucleotide-free state.
Voxel size
X=Y=Z: 0.86 Å
Density
Contour Level
By AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum
-0.06988939 - 0.22754554
Average (Standard dev.)
0.0021357222 (±0.02195315)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
256
256
256
Spacing
256
256
256
Cell
A=B=C: 220.16 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
0.86
0.86
0.86
M x/y/z
256
256
256
origin x/y/z
0.000
0.000
0.000
length x/y/z
220.160
220.160
220.160
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
256
256
256
D min/max/mean
-0.070
0.228
0.002
-
Supplemental data
-
Additional map: A symmetry-free cryo-EM structure of a single-ring chaperonin...
A symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the nucleotide-free state.
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