+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33187 | |||||||||
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Title | Structure of Gemin5 C-terminal region (protomer) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA binding / TPR repeats / decamer / RNA translation / RNA BINDING PROTEIN | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Guo Q / Zhao S / Zhang K / Xu C | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33187.map.gz | 62.7 MB | EMDB map data format | |
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Header (meta data) | emd-33187-v30.xml emd-33187.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_33187.png | 68.8 KB | ||
Filedesc metadata | emd-33187.cif.gz | 5.5 KB | ||
Others | emd_33187_half_map_1.map.gz emd_33187_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33187 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33187 | HTTPS FTP |
-Validation report
Summary document | emd_33187_validation.pdf.gz | 644.9 KB | Display | EMDB validaton report |
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Full document | emd_33187_full_validation.pdf.gz | 644.5 KB | Display | |
Data in XML | emd_33187_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_33187_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33187 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33187 | HTTPS FTP |
-Related structure data
Related structure data | 7xgrMC 7xdtC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33187.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33187_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33187_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Gemin5
Entire | Name: Gemin5 |
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Components |
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-Supramolecule #1: Gemin5
Supramolecule | Name: Gemin5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 750 kDa/nm |
-Macromolecule #1: Gem-associated protein 5
Macromolecule | Name: Gem-associated protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 75.893875 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 UniProtKB: Gem-associated protein 5 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8709340 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |