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- EMDB-33152: Structural basis for Gemin5 decamer-mediated mRNA binding -

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Basic information

Entry
Database: EMDB / ID: EMD-33152
TitleStructural basis for Gemin5 decamer-mediated mRNA binding
Map data
Sample
  • Complex: Gemin5Gem-associated protein 5
    • Protein or peptide: Gem-associated protein 5
Function / homology
Function and homology information


SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding ...SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / ribosome binding / regulation of translation / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / protein-containing complex assembly / nuclear body / translation / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
MIOS, WD40 repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...MIOS, WD40 repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsGuo Q / Zhao S / Zhang K / Xu C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for Gemin5 decamer-mediated mRNA binding.
Authors: Qiong Guo / Shidong Zhao / Rosario Francisco-Velilla / Jiahai Zhang / Azman Embarc-Buh / Salvador Abellan / Mengqi Lv / Peiping Tang / Qingguo Gong / Huaizong Shen / Linfeng Sun / Xuebiao ...Authors: Qiong Guo / Shidong Zhao / Rosario Francisco-Velilla / Jiahai Zhang / Azman Embarc-Buh / Salvador Abellan / Mengqi Lv / Peiping Tang / Qingguo Gong / Huaizong Shen / Linfeng Sun / Xuebiao Yao / Jinrong Min / Yunyu Shi / Encarnacion Martínez-Salas / Kaiming Zhang / Chao Xu /
Abstract: Gemin5 in the Survival Motor Neuron (SMN) complex serves as the RNA-binding protein to deliver small nuclear RNAs (snRNAs) to the small nuclear ribonucleoprotein Sm complex via its N-terminal WD40 ...Gemin5 in the Survival Motor Neuron (SMN) complex serves as the RNA-binding protein to deliver small nuclear RNAs (snRNAs) to the small nuclear ribonucleoprotein Sm complex via its N-terminal WD40 domain. Additionally, the C-terminal region plays an important role in regulating RNA translation by directly binding to viral RNAs and cellular mRNAs. Here, we present the three-dimensional structure of the Gemin5 C-terminal region, which adopts a homodecamer architecture comprised of a dimer of pentamers. By structural analysis, mutagenesis, and RNA-binding assays, we find that the intact pentamer/decamer is critical for the Gemin5 C-terminal region to bind cognate RNA ligands and to regulate mRNA translation. The Gemin5 high-order architecture is assembled via pentamerization, allowing binding to RNA ligands in a coordinated manner. We propose a model depicting the regulatory role of Gemin5 in selective RNA binding and translation. Therefore, our work provides insights into the SMN complex-independent function of Gemin5.
History
DepositionMar 28, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33152.png

Downloads & links

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Map

FileDownload / File: emd_33152.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.6121343 - 1.1302614
Average (Standard dev.)0.0013142903 (±0.030125957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33152_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33152_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gemin5

EntireName: Gemin5Gem-associated protein 5
Components
  • Complex: Gemin5Gem-associated protein 5
    • Protein or peptide: Gem-associated protein 5

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Supramolecule #1: Gemin5

SupramoleculeName: Gemin5 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 750 kDa/nm

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Macromolecule #1: Gem-associated protein 5

MacromoleculeName: Gem-associated protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.893875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMKKRKARS LLPLSTSLDH RSKEELHQDC LVLATAKHSR ELNEDVSADV EERFHLGLFT DRATLYRMID IEGKGHLENG HPELFHQLM LWKGDLKGVL QTAAERGELT DNLVAMAPAA GYHVWLWAVE AFAKQLCFQD QYVKAASHLL SIHKVYEAVE L LKSNHFYR ...String:
GHMKKRKARS LLPLSTSLDH RSKEELHQDC LVLATAKHSR ELNEDVSADV EERFHLGLFT DRATLYRMID IEGKGHLENG HPELFHQLM LWKGDLKGVL QTAAERGELT DNLVAMAPAA GYHVWLWAVE AFAKQLCFQD QYVKAASHLL SIHKVYEAVE L LKSNHFYR EAIAIAKARL RPEDPVLKDL YLSWGTVLER DGHYAVAAKC YLGATCAYDA AKVLAKKGDA ASLRTAAELA AI VGEDELS ASLALRCAQE LLLANNWVGA QEALQLHESL QGQRLVFCLL ELLSRHLEEK QLSEGKSSSS YHTWNTGTEG PFV ERVTAV WKSIFSLDTP EQYQEAFQKL QNIKYPSATN NTPAKQLLLH ICHDLTLAVL SQQMASWDEA VQALLRAVVR SYDS GSFTI MQEVYSAFLP DGCDHLRDKL GDHQSPATPA FKSLEAFFLY GRLYEFWWSL SRPCPNSSVW VRAGHRTLSV EPSQQ LDTA STEETDPETS QPEPNRPSEL DLRLTEEGER MLSTFKELFS EKHASLQNSQ RTVAEVQETL AEMIRQHQKS QLCKST ANG PDKNEPEVEA EQPLCSSQSQ CKEEKNEPLS LPELTKRLTE ANQRMAKFPE SIKAWPFPDV LECCLVLLLI RSHFPGC LA QEMQQQAQEL LQKYGNTKTY RRHCQTFCM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 8.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rnq

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 870934

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