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- PDB-7xgr: Structure of Gemin5 C-terminal region (protomer) -

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Basic information

Entry
Database: PDB / ID: 7xgr
TitleStructure of Gemin5 C-terminal region (protomer)
ComponentsGem-associated protein 5
KeywordsRNA BINDING PROTEIN / RNA binding / TPR repeats / decamer / RNA translation
Function / homology
Function and homology information


SMN-Gemin2 complex / Gemini of Cajal bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / SMN-Sm protein complex / U4 snRNA binding / spliceosomal snRNP assembly / U1 snRNA binding ...SMN-Gemin2 complex / Gemini of Cajal bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / SMN-Sm protein complex / U4 snRNA binding / spliceosomal snRNP assembly / U1 snRNA binding / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / regulation of translation / ribosome binding / protein-containing complex assembly / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / translation / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / : / : / : / RIG first beta-propeller / GEMI5 TPR domain / RIG second beta-propeller / GEMI5 RBS C-terminal domain / Quinoprotein alcohol dehydrogenase-like superfamily ...: / : / : / : / : / RIG first beta-propeller / GEMI5 TPR domain / RIG second beta-propeller / GEMI5 RBS C-terminal domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGuo, Q. / Zhao, S. / Zhang, K. / Xu, C.
Funding support China, 1items
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
DepositionApr 6, 2022Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gem-associated protein 5


Theoretical massNumber of molelcules
Total (without water)75,8941
Polymers75,8941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Gem-associated protein 5 / Gemin5


Mass: 75893.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TEQ6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Gemin5 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 750 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8709340 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044450
ELECTRON MICROSCOPYf_angle_d0.5916024
ELECTRON MICROSCOPYf_dihedral_angle_d4.497585
ELECTRON MICROSCOPYf_chiral_restr0.036671
ELECTRON MICROSCOPYf_plane_restr0.003769

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