[English] 日本語
Yorodumi
- EMDB-40986: Structure of a group II intron ribonucleoprotein in the pre-branc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40986
TitleStructure of a group II intron ribonucleoprotein in the pre-branching (pre-1F) state
Map dataOverall refined map for pre-1f
Sample
  • Complex: Intron RNP complex in pre-1f
    • Protein or peptide: Group II intron reverse transcriptase/maturase
    • RNA: RNA (551-MER)
  • Ligand: CALCIUM ION
  • Ligand: AMMONIUM ION
KeywordsRNP / RNA / Transferase-RNA complex
Function / homology
Function and homology information


RNA-directed DNA polymerase / RNA-directed DNA polymerase activity
Similarity search - Function
Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / : / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Group II intron reverse transcriptase/maturase
Similarity search - Component
Biological species[Eubacterium] rectale (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsXu L / Liu T / Chung K / Pyle AM
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2023
Title: Structural insights into intron catalysis and dynamics during splicing.
Authors: Ling Xu / Tianshuo Liu / Kevin Chung / Anna Marie Pyle /
Abstract: The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns. Despite the importance of ...The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns. Despite the importance of branching in RNA metabolism, structural understanding of this process has remained elusive. Here we present a comprehensive analysis of three single-particle cryogenic electron microscopy structures captured along the splicing pathway. They reveal the network of molecular interactions that specifies the branchpoint adenosine and positions key functional groups to catalyse lariat formation and coordinate exon ligation. The structures also reveal conformational rearrangements of the branch helix and the mechanism of splice site exchange that facilitate the transition from branching to ligation. These findings shed light on the evolution of splicing and highlight the conservation of structural components, catalytic mechanism and dynamical strategies retained through time in premessenger RNA splicing machines.
History
DepositionJun 6, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40986.png

Downloads & links

-
Map

FileDownload / File: emd_40986.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall refined map for pre-1f
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.3329468 - 1.9797381
Average (Standard dev.)0.000977606 (±0.0324515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 324.096 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_40986_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_40986_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Locally refined map (right) for pre-1f

Fileemd_40986_additional_1.map
AnnotationLocally refined map (right) for pre-1f
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Locally refined map (left) for pre-1f

Fileemd_40986_additional_2.map
AnnotationLocally refined map (left) for pre-1f
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Overall map (half A)

Fileemd_40986_half_map_1.map
AnnotationOverall map (half_A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Overall map (half B)

Fileemd_40986_half_map_2.map
AnnotationOverall map (half_B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Intron RNP complex in pre-1f

EntireName: Intron RNP complex in pre-1f
Components
  • Complex: Intron RNP complex in pre-1f
    • Protein or peptide: Group II intron reverse transcriptase/maturase
    • RNA: RNA (551-MER)
  • Ligand: CALCIUM ION
  • Ligand: AMMONIUM ION

-
Supramolecule #1: Intron RNP complex in pre-1f

SupramoleculeName: Intron RNP complex in pre-1f / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 300 KDa

-
Macromolecule #1: Group II intron reverse transcriptase/maturase

MacromoleculeName: Group II intron reverse transcriptase/maturase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 49.083914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDTSNLMEQI LSSDNLNRAY LQVVRNKGAE GVDGMKYTEL KEHLAKNGET IKGQLRTRKY KPQPARRVEI PKPDGGVRNL GVPTVTDRF IQQAIAQVLT PIYEEQFHDH SYGFRPNRCA QQAILTALNI MNDGNDWIVD IDLEKFFDTV NHDKLMTLIG R TIKDGDVI ...String:
MDTSNLMEQI LSSDNLNRAY LQVVRNKGAE GVDGMKYTEL KEHLAKNGET IKGQLRTRKY KPQPARRVEI PKPDGGVRNL GVPTVTDRF IQQAIAQVLT PIYEEQFHDH SYGFRPNRCA QQAILTALNI MNDGNDWIVD IDLEKFFDTV NHDKLMTLIG R TIKDGDVI SIVRKYLVSG IMIDDEYEDS IVGTPQGGNL SPLLANIMLN ELDKEMEKRG LNFVRYADDC IIMVGSEMSA NR VMRNISR FIEEKLGLKV NMTKSKVDRP SGLKYLGFGF YFDPRAHQFK AKPHAKSVAK FKKRMKELTC RSWGVSNSYK VEK LNQLIR GWINYFKIGS MKTLCKELDS RIRYRLRMCI WKQWKTPQNQ EKNLVKLGID RNTARRVAYT GKRIAYVCNK GAVN VAISN KRLASFGLIS MLDYYIEKCV TC

UniProtKB: Group II intron reverse transcriptase/maturase

-
Macromolecule #2: RNA (551-MER)

MacromoleculeName: RNA (551-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 211.194406 KDa
SequenceString: GAGCUCAUUU CUUUGUUUGC GCGCCAUGGG CGCGCUCUAA CGGGUGUAAG UCCCGAACAU GCCCAGGUAG UGGGAAAUGU AUAGCCGAA CAGCAAGGGU GUCUACUGUG AGGUGGAAUC UGAAGGAAGC UGUAAGCGAA UCUCUGGUCC GACGGACAGA A AUCGCAUA ...String:
GAGCUCAUUU CUUUGUUUGC GCGCCAUGGG CGCGCUCUAA CGGGUGUAAG UCCCGAACAU GCCCAGGUAG UGGGAAAUGU AUAGCCGAA CAGCAAGGGU GUCUACUGUG AGGUGGAAUC UGAAGGAAGC UGUAAGCGAA UCUCUGGUCC GACGGACAGA A AUCGCAUA UAAGGCUAGG CUUCGAGUGA UAAGCUGGCA AAGAACAGUG AAGUCUAAUA ACUACCACGU UUGUAGAAGC AG AGUAAAU GCGGCGGAUA UAUGGAGAGA AAGAGCGUGC ACCUUAAGCG UGGAGGUCUC ACAGAGGUUU CAUUAGCCUA GUA ACAACG AACUGUGAGA AGUCAGCCGA GCCCAUAGUA GUGAAGAAGU CUCUGUAAUG GGGAUGGAGC GAAGGGGCGA ACAA UCAAU CAGUUUGAGA AUGUCUCGUA UUGCAGAAAU GACAACAUCU GCCGUAACCA AUCGGGUAAA AGGUGGUCAA AUCAA GCGA GACGGAAAGG AAAGAACGCA UGGACACAAG UAAUCUAAUU UCGGUUAGAU UACUACAUCG AAAAGUGUGU UACUUG UUA AAUUGAUUGA ACCGCCGUAU ACGGAACCGU ACGUACGGUG GUGUGAGAGG UCGGAAUUUC UCAAUUAAGA GAAAUUC UU CCUACUCGAU

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 11 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #4: AMMONIUM ION

MacromoleculeName: AMMONIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: NH4
Molecular weightTheoretical: 18.038 Da
Chemical component information

ChemComp-NH4:
AMMONIUM ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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

7uin

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 261619
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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