[English] 日本語
Yorodumi
- EMDB-28536: FAM46C/BCCIPalpha/Nanobody complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28536
TitleFAM46C/BCCIPalpha/Nanobody complex
Map data
Sample
  • Complex: the complex between FAM46C and BCCIPalpha
    • Protein or peptide: Synthetic nanobody 1
    • Protein or peptide: Terminal nucleotidyltransferase 5C
    • Protein or peptide: Isoform 2 of BRCA2 and CDKN1A-interacting protein
KeywordsFAM46 / BCCIP / poly-A polymerase / alternative splicing / NUCLEAR PROTEIN
Function / homology
Function and homology information


polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA stabilization / negative regulation of cell differentiation / in utero embryonic development / centrosome / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Terminal nucleotidyltransferase / Nucleotidyltransferase / Domain of unknown function (DUF1693)
Similarity search - Domain/homology
Terminal nucleotidyltransferase 5C / Isoform 2 of BRCA2 and CDKN1A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsLiu S / Chen H / Yin Y / Bai X / Zhang X
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA220283 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143158 United States
Welch FoundationI-1702 United States
Welch FoundationI-1944 United States
CitationJournal: 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
DepositionOct 7, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28536.png

Downloads & links

-
Map

FileDownload / File: emd_28536.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.0062977304 - 0.031955514
Average (Standard dev.)0.00064989395 (±0.002662233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_28536_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28536_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : the complex between FAM46C and BCCIPalpha

EntireName: the complex between FAM46C and BCCIPalpha
Components
  • Complex: the complex between FAM46C and BCCIPalpha
    • Protein or peptide: Synthetic nanobody 1
    • Protein or peptide: Terminal nucleotidyltransferase 5C
    • Protein or peptide: Isoform 2 of BRCA2 and CDKN1A-interacting protein

-
Supramolecule #1: the complex between FAM46C and BCCIPalpha

SupramoleculeName: the complex between FAM46C and BCCIPalpha / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

-
Macromolecule #1: Synthetic nanobody 1

MacromoleculeName: Synthetic nanobody 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.719396 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPHMQVQLQE SGGGLVQAGG SLRLSCAASG TISPRGVMGW YRQAPGKERE FVAAINYGGT TYYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC AVYYYINSQR KVLLYWGQGT QVTVSS

-
Macromolecule #2: Terminal nucleotidyltransferase 5C

MacromoleculeName: Terminal nucleotidyltransferase 5C / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: polynucleotide adenylyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.533254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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)

UniProtKB: Terminal nucleotidyltransferase 5C

-
Macromolecule #3: Isoform 2 of BRCA2 and CDKN1A-interacting protein

MacromoleculeName: Isoform 2 of BRCA2 and CDKN1A-interacting protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.190066 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Isoform 2 of BRCA2 and CDKN1A-interacting protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7376
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more