Journal: Protein Cell / Year: 2016 Title: Structural dynamics of the yeast Shwachman-Diamond syndrome protein (Sdo1) on the ribosome and its implication in the 60S subunit maturation. Authors: Chengying Ma / Kaige Yan / Dan Tan / Ningning Li / Yixiao Zhang / Yi Yuan / Zhifei Li / Meng-Qiu Dong / Jianlin Lei / Ning Gao / Abstract: The human Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease caused by mutations in a highly conserved ribosome assembly factor SBDS. The functional role of SBDS is to cooperate with ...The human Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease caused by mutations in a highly conserved ribosome assembly factor SBDS. The functional role of SBDS is to cooperate with another assembly factor, elongation factor 1-like (Efl1), to promote the release of eukaryotic initiation factor 6 (eIF6) from the late-stage cytoplasmic 60S precursors. In the present work, we characterized, both biochemically and structurally, the interaction between the 60S subunit and SBDS protein (Sdo1p) from yeast. Our data show that Sdo1p interacts tightly with the mature 60S subunit in vitro through its domain I and II, and is capable of bridging two 60S subunits to form a stable 2:2 dimer. Structural analysis indicates that Sdo1p bind to the ribosomal P-site, in the proximity of uL16 and uL5, and with direct contact to H69 and H38. The dynamic nature of Sdo1p on the 60S subunit, together with its strategic binding position, suggests a surveillance role of Sdo1p in monitoring the conformational maturation of the ribosomal P-site. Altogether, our data support a conformational signal-relay cascade during late-stage 60S maturation, involving uL16, Sdo1p, and Efl1p, which interrogates the functional P-site to control the departure of the anti-association factor eIF6.
History
Deposition
Dec 11, 2015
-
Header (metadata) release
Jan 27, 2016
-
Map release
Mar 30, 2016
-
Update
Mar 30, 2016
-
Current status
Mar 30, 2016
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_3280.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Reconstruction of 60S-Sdo1p complex.
Voxel size
X=Y=Z: 2.76 Å
Density
Contour Level
By AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum
-0.03258364 - 0.11587372
Average (Standard dev.)
-0.00059538 (±0.01439751)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
180
180
180
Spacing
180
180
180
Cell
A=B=C: 496.8 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.76
2.76
2.76
M x/y/z
180
180
180
origin x/y/z
0.000
0.000
0.000
length x/y/z
496.800
496.800
496.800
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
180
180
180
D min/max/mean
-0.033
0.116
-0.001
-
Supplemental data
-
Sample components
-
Entire : The dimeric structure of the yeast 60S ribosomal subunits bound w...
Entire
Name: The dimeric structure of the yeast 60S ribosomal subunits bound with Sdo1p
Components
Sample: The dimeric structure of the yeast 60S ribosomal subunits bound with Sdo1p
Complex: Sdo1p bound 60S subunit
Protein or peptide: Sdo1p
-
Supramolecule #1000: The dimeric structure of the yeast 60S ribosomal subunits bound w...
Supramolecule
Name: The dimeric structure of the yeast 60S ribosomal subunits bound with Sdo1p type: sample / ID: 1000 / Oligomeric state: two Sdo1p binding to two 60S subunit / Number unique components: 2
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