[English] 日本語
Yorodumi
- EMDB-29279: Cryo-EM structure of a group II intron immediately before branching -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29279
TitleCryo-EM structure of a group II intron immediately before branching
Map data
Sample
  • Complex: Group IIB intron in complex with its maturase protein
    • RNA: Group II Intron
    • Protein or peptide: Maturase reverse transcriptase
  • Ligand: MAGNESIUM ION
Keywordsgroup II intron / splicing / branching / maturase / SPLICING-RNA complex
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / endonuclease activity / nucleic acid binding / zinc ion binding
Similarity search - Function
Reverse transcriptase, N-terminal domain / N-terminal domain of reverse transcriptase / Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / HNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / Reverse transcriptase (RNA-dependent DNA polymerase) ...Reverse transcriptase, N-terminal domain / N-terminal domain of reverse transcriptase / Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / HNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Maturase reverse transcriptase
Similarity search - Component
Biological speciesThermosynechococcus vestitus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHaack DB / Rudolfs BG / Zhang C / Lyumkis D / Toor N
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of branching during RNA splicing.
Authors: Daniel B Haack / Boris Rudolfs / Cheng Zhang / Dmitry Lyumkis / Navtej Toor /
Abstract: Branching is a critical step in RNA splicing that is essential for 5' splice site selection. Recent spliceosome structures have led to competing models for the recognition of the invariant adenosine ...Branching is a critical step in RNA splicing that is essential for 5' splice site selection. Recent spliceosome structures have led to competing models for the recognition of the invariant adenosine at the branch point. However, there are no structures of any splicing complex with the adenosine nucleophile docked in the active site and positioned to attack the 5' splice site. Thus we lack a mechanistic understanding of adenosine selection and splice site recognition during RNA splicing. Here we present a cryo-electron microscopy structure of a group II intron that reveals that active site dynamics are coupled to the formation of a base triple within the branch-site helix that positions the 2'-OH of the adenosine for nucleophilic attack on the 5' scissile phosphate. This structure, complemented with biochemistry and comparative analyses to splicing complexes, supports a base triple model of adenosine recognition for branching within group II introns and the evolutionarily related spliceosome.
History
DepositionDec 21, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29279.png

Downloads & links

-
Map

FileDownload / File: emd_29279.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.8479088 - 1.6336483
Average (Standard dev.)0.0008706103 (±0.045878638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_29279_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_29279_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Group IIB intron in complex with its maturase protein

EntireName: Group IIB intron in complex with its maturase protein
Components
  • Complex: Group IIB intron in complex with its maturase protein
    • RNA: Group II Intron
    • Protein or peptide: Maturase reverse transcriptase
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Group IIB intron in complex with its maturase protein

SupramoleculeName: Group IIB intron in complex with its maturase protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Thermosynechococcus vestitus (bacteria)

-
Macromolecule #1: Group II Intron

MacromoleculeName: Group II Intron / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Thermosynechococcus vestitus (bacteria)
Molecular weightTheoretical: 289.257938 KDa
SequenceString: CCCAGGGUUG GCCGAGCGUU GCGACGCGAA AGCUAGCCAG AUGAUUGUCC CACUAGCCCA ACAAGCUAGA ACGGGACCGG UUGUUCCCC CAACCGUAGC CUAGGGAGGC AUGCGUGACU GGUAACGGUC AGGUGUGAAG CCCUCCCGAC AAUGUAGCCC G AACCGCAA ...String:
CCCAGGGUUG GCCGAGCGUU GCGACGCGAA AGCUAGCCAG AUGAUUGUCC CACUAGCCCA ACAAGCUAGA ACGGGACCGG UUGUUCCCC CAACCGUAGC CUAGGGAGGC AUGCGUGACU GGUAACGGUC AGGUGUGAAG CCCUCCCGAC AAUGUAGCCC G AACCGCAA GGUUGAAGCU GAAUCCGUGA GGAGGAAGCA ACUUCACCAG UGUCAGGUGA UAGGGAACUA GGCUUGAGGG UA UGGUGAG CACAUGCGAA GUGAUGUCAG AAGCCUCGUC ACAGACCAAC AGGCCAAAGA CACUGAUAGG CCUGAGCCAA AAC GGCAAA UGGAUAGGCU ACAUCGCUCG CUCGUCGGUG UACGGGGACG UCAAUCCAUC GGGGCACAGU CACCACCUAA CCCC UCGUG UCAUCUGGUU GGAACGCGGU AAGCCCGUAU CCUCGCCUUG AACACUCAAG GCAGGCAAAC CUUCGGGAAU GCUGA UGGG GGUGCGGGUA UGGGAUGCAG GAGAAAGCGA AUGCCGGUCU GUAAUGGACC GGAUAGGGGU UGAGGAGACA AUCCAA CAU CACCCCGCCC GAAAGGGAGC AGACUUCCUG CUGGUCUCUC UUUGCGAGAU AGCCUGUAGA ACCUCUUGAA UGGAGAC AA GGCAAAUGGC AGUGGAACAA ACCACUGGUG CGGUCACCAA CCAAACGGAA ACAAGCUGGC ACAGCAUAGA CUGGGCCA A AGCCAACCGU GAGGUAAAGA GGCUGCAAGU GCGUAUCGCA AAGGCGUUCG CGCCGGUUCC UCUUGAAAGA GGGGCUUUG AGAGGCCUGA GCCGGAUGUG GGGAAACUCA CAAGUCCGGU UCUUAGGGGG CGGGGAUGGC AUUCGUGCCU CCCUGCUACC CGGCGAUGA GGCA

-
Macromolecule #2: Maturase reverse transcriptase

MacromoleculeName: Maturase reverse transcriptase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus (bacteria)
Molecular weightTheoretical: 65.065121 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: METRQMAVEQ TTGAVTNQTE TSWHSIDWAK ANREVKRLQV RIAKAVKEGR WGKVKALQWL LTHSFYGKAL AVKRVTDNSG SKTPGVDGI TWSTQEQKAQ AIKSLRRRGY KPQPLRRVYI PKASGKQRPL GIPTTKDRAM QALYALALEP VAETTADRNS Y GFRQGRCT ...String:
METRQMAVEQ TTGAVTNQTE TSWHSIDWAK ANREVKRLQV RIAKAVKEGR WGKVKALQWL LTHSFYGKAL AVKRVTDNSG SKTPGVDGI TWSTQEQKAQ AIKSLRRRGY KPQPLRRVYI PKASGKQRPL GIPTTKDRAM QALYALALEP VAETTADRNS Y GFRQGRCT ADAAGQCFTV LGRSDCAKYI LDADITGCFD NISHEWLLDN IPLDKEVLRK WLKSGFVWKQ QLFPTHAGTP QG GVISPML ANMTLDGMEE LLKKHLRKQK VNLIRYADDF VVTGESKETL EKVTTVIQEF LKERGLTLSE EKTKVVHIEE GFD FLGWNI RKYGEKLLIK PAKKNIKAFH KKIRDALKEL RTATQEAVID TLNPIIKGWA NYHRNQVSKR IFNRADDNIW HKLW RWAKR RHPNKPARWT KNKYFIKIGN RHWVFGTWKK DKEGRLRSRY LIKAGDTRIQ RHVKIKADAN PFLPEWAEYF EERKK LKEA PAQYRRIRRE LWKKQGGICP VCGGEIEQDM LTEIHHILPK HKGGSDDLDN LVLIHANCHK QVHSRDGQHS RFLLKE GL

UniProtKB: Maturase reverse transcriptase

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 31.6 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

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

6mec

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38881

+
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