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- EMDB-38550: Cryo-EM structure of the human 40S ribosome with LARP1 (LARP1 pul... -

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Basic information

Entry
Database: EMDB / ID: EMD-38550
TitleCryo-EM structure of the human 40S ribosome with LARP1 (LARP1 pull out)
Map datamap without post process
Sample
  • Complex: LARP1-40S ribosome (LARP1 pull out)
Keywords40S ribosome / LARP1 / mTOR / LRRC47 / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHuang Z / Ye X / Li Y / Cheng J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: EMBO J / Year: 2024
Title: LARP1 binds ribosomes and TOP mRNAs in repressed complexes.
Authors: James A Saba / Zixuan Huang / Kate L Schole / Xianwen Ye / Shrey D Bhatt / Yi Li / Winston Timp / Jingdong Cheng / Rachel Green /
Abstract: Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies have implicated LARP1 in ...Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies have implicated LARP1 in 40S- or 80S-ribosome complexes that are thought to repress and stabilize TOPs. However, a molecular understanding of how LARP1 and TOPs interact with these ribosome complexes is lacking. Here, we show that LARP1 directly binds non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the mRNA channel of the 40S subunit. Increased availability of free ribosomal subunits downstream of various stresses promote 60S joining at the same interface to form LARP1-80S complexes. Simultaneously, LARP1 engages the TOP via its previously characterized La/PAM2 and DM15 domains. Contrary to expectations, ribosome binding within these complexes is not required for LARP1-mediated TOP repression or stabilization, two canonical LARP1 functions. Together, this work provides molecular insight into how LARP1 directly binds ribosomal subunits and challenges existing models describing the function of repressed LARP1-40S/80S-TOP complexes.
History
DepositionJan 2, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38550.png

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Map

FileDownload / File: emd_38550.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap without post process
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Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 447.36 Å		0.93 Å/pix.
x 480 pix.
= 447.36 Å		0.93 Å/pix.
x 480 pix.
= 447.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
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Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.3570303 - 2.8733618
Average (Standard dev.)0.006728367 (±0.07492211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 447.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38550_msk_1.map
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Additional map: map local resolution filtered using Relion

Fileemd_38550_additional_1.map
Annotationmap local resolution filtered using Relion
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Half map: #1

Fileemd_38550_half_map_1.map
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Half map: #2

Fileemd_38550_half_map_2.map
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Sample components

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Entire : LARP1-40S ribosome (LARP1 pull out)

EntireName: LARP1-40S ribosome (LARP1 pull out)
Components
  • Complex: LARP1-40S ribosome (LARP1 pull out)

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Supramolecule #1: LARP1-40S ribosome (LARP1 pull out)

SupramoleculeName: LARP1-40S ribosome (LARP1 pull out) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#37 / Details: 40S ribosome with LARP1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 518116
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 107728
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.2) / Details: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.2) / Details: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6z6m


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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