Journal: Nat Commun / Year: 2020 Title: MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments. Authors: Klemens Wild / Milan Aleksić / Karine Lapouge / Keven D Juaire / Dirk Flemming / Stefan Pfeffer / Irmgard Sinning / Abstract: Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature ...Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature 80S ribosomes for translational control. Here, we present a cryo-EM single particle analysis reconstruction of Ebp1 bound to non-translating human 80S ribosomes at a resolution range from 3.3 to ~8 Å. Ebp1 blocks the tunnel exit with major interactions to the general uL23/uL29 docking site for nascent chain-associated factors complemented by eukaryote-specific eL19 and rRNA helix H59. H59 is defined as dynamic adaptor undergoing significant remodeling upon Ebp1 binding. Ebp1 recruits rRNA expansion segment ES27L to the tunnel exit via specific interactions with rRNA consensus sequences. The Ebp1-ribosome complex serves as a template for MetAP binding and provides insights into the structural principles for spatial coordination of co-translational events and molecular triage at the ribosomal tunnel exit.
History
Deposition
Jan 14, 2020
-
Header (metadata) release
Feb 19, 2020
-
Map release
Feb 19, 2020
-
Update
Feb 19, 2020
-
Current status
Feb 19, 2020
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_10609.map.gz / Format: CCP4 / Size: 181 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
None
Voxel size
X=Y=Z: 1.5218 Å
Density
Contour Level
By AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum
-1.197571 - 1.5386089
Average (Standard dev.)
0.00004733595 (±0.0043876353)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-1
-1
-1
Dimensions
362
362
362
Spacing
362
362
362
Cell
A=B=C: 550.8916 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.5218011049724
1.5218011049724
1.5218011049724
M x/y/z
362
362
362
origin x/y/z
0.000
0.000
0.000
length x/y/z
550.892
550.892
550.892
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
-1
-1
-1
NC/NR/NS
362
362
362
D min/max/mean
-1.198
1.539
0.000
-
Supplemental data
-
Sample components
-
Entire : Human Ebp1-ribosome complex
Entire
Name: Human Ebp1-ribosome complex
Components
Complex: Human Ebp1-ribosome complex
-
Supramolecule #1: Human Ebp1-ribosome complex
Supramolecule
Name: Human Ebp1-ribosome complex / type: complex / ID: 1 / Parent: 0 Details: Puromycin-treated ribosomes from HeLa cells in complex with recombinantly expressed Ebp1
Source (natural)
Organism: Homo sapiens (human)
Recombinant expression
Organism: Escherichia coli (E. coli)
-
Experimental details
-
Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Buffer
pH: 7.5 Details: 20 mM HEPES KOH pH 7.5 5 mM Mg(OAc)2 175 mM KOAc 1 mM Tris(2-carboxyethyl)phosphin
Grid
Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Details
100 nM ribosome; 800 nM Ebp1
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3370 / Average electron dose: 38.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) Details: ES27L-Ebp1 density segment after 3-body multibody refinement; filtered according to local resolution Number images used: 34467
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classification
Software - Name: RELION (ver. 3.0)
+
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