+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28536 | |||||||||||||||
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Title | FAM46C/BCCIPalpha/Nanobody complex | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information mRNA stabilization / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / negative regulation of cell differentiation / in utero embryonic development / centrosome / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||||||||
Authors | Liu S / Chen H / Yin Y / Bai X / Zhang X | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. Authors: Shun Liu / Hua Chen / Yan Yin / Defen Lu / Guoming Gao / Jie Li / Xiao-Chen Bai / Xuewu Zhang / Abstract: The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report ...The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28536.map.gz | 3.7 MB | EMDB map data format | |
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Header (meta data) | emd-28536-v30.xml emd-28536.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28536_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_28536.png | 57.9 KB | ||
Others | emd_28536_half_map_1.map.gz emd_28536_half_map_2.map.gz | 22.3 MB 22.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28536 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28536 | HTTPS FTP |
-Related structure data
Related structure data | 8eqbMC 8exeC 8exfC 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_28536.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28536_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28536_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the complex between FAM46C and BCCIPalpha
Entire | Name: the complex between FAM46C and BCCIPalpha |
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Components |
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-Supramolecule #1: the complex between FAM46C and BCCIPalpha
Supramolecule | Name: the complex between FAM46C and BCCIPalpha / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Synthetic nanobody 1
Macromolecule | Name: Synthetic nanobody 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 13.719396 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPHMQVQLQE SGGGLVQAGG SLRLSCAASG TISPRGVMGW YRQAPGKERE FVAAINYGGT TYYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC AVYYYINSQR KVLLYWGQGT QVTVSS |
-Macromolecule #2: Terminal nucleotidyltransferase 5C
Macromolecule | Name: Terminal nucleotidyltransferase 5C / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: polynucleotide adenylyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.533254 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGAPSVLNW DQVSRLHEVL TEVVPIHGRG NFPTLEITLK DIVQTVRSRL EEAGIKVHDV RLNGSAAGHV LVKDNGLGCK DLDLIFHVA LPTEAEFQLV RDVVLCSLLN FLPEGVNKLK ISPVTLKEAY VQKLVKVCTD TDRWSLISLS NKNGKNVQLK F VDSIRRQF ...String: GPGAPSVLNW DQVSRLHEVL TEVVPIHGRG NFPTLEITLK DIVQTVRSRL EEAGIKVHDV RLNGSAAGHV LVKDNGLGCK DLDLIFHVA LPTEAEFQLV RDVVLCSLLN FLPEGVNKLK ISPVTLKEAY VQKLVKVCTD TDRWSLISLS NKNGKNVQLK F VDSIRRQF EFSVDSFQII LDSLLFFYDC SNNPISEHFH PTVIGES(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: Isoform 2 of BRCA2 and CDKN1A-interacting protein
Macromolecule | Name: Isoform 2 of BRCA2 and CDKN1A-interacting protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.190066 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGAPDEVID EEVNIEFEAY SLSDNDYDGI KKLLQQLFLK APVNTAELTD LLIQQNHIGS VIKQTDVEVF GFISLLNLTE RKGTQCVEQ IQELVLRFCE KNCEKSMVEQ LDKFLNDTTK PVGLLLSERF INVPPQIALP MYQQLQKELA GAHRTNKPCG K CYFYLLIS ...String: GPGAPDEVID EEVNIEFEAY SLSDNDYDGI KKLLQQLFLK APVNTAELTD LLIQQNHIGS VIKQTDVEVF GFISLLNLTE RKGTQCVEQ IQELVLRFCE KNCEKSMVEQ LDKFLNDTTK PVGLLLSERF INVPPQIALP MYQQLQKELA GAHRTNKPCG K CYFYLLIS KTFVEAGKNN SAALMFANAE EEFFYEEQGK PEVLGGPDTR PVPIQHNGGS RGQVTALVSL KAGLIQSRST LS DFQGTFM TVGIALS |
-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: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |