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- PDB-6me0: Structure of a group II intron retroelement prior to DNA integration -

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Basic information

Entry
Database: PDB / ID: 6me0
TitleStructure of a group II intron retroelement prior to DNA integration
Components
  • Maturase reverse transcriptase
  • Sense Target DNA
  • T.el4h RNA
KeywordsRNA/DNA/Nucleic Acid Binding protein / Group II intron / Retroelement / Retrotransposition / RNA-DNA-Nucleic Acid Binding protein 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, 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 domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Maturase reverse transcriptase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHaack, D. / Yan, X. / Zhang, C. / Hingey, J. / Lyumkis, D. / Baker, T.S. / Toor, N.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM033050 United States
National Institutes of Health/Office of the DirectorDP5 OD021396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM103368 United States
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.
Authors: Daniel B Haack / Xiaodong Yan / Cheng Zhang / Jason Hingey / Dmitry Lyumkis / Timothy S Baker / Navtej Toor /
Abstract: Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a ...Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a maturase protein, which promotes splicing through an unknown mechanism. The mechanism of splice site exchange within the RNA active site during catalysis also remains unclear. We determined two cryo-EM structures at 3.6-Å resolution of a group II intron reverse splicing into DNA. These structures reveal that the branch-site domain VI helix swings 90°, enabling substrate exchange during DNA integration. The maturase assists catalysis through a transient RNA-protein contact with domain VI that positions the branch-site adenosine for lariat formation during forward splicing. These findings provide the first direct evidence of the role the maturase plays during group II intron catalysis. The domain VI dynamics closely parallel spliceosomal branch-site helix movement and provide strong evidence for a retroelement origin of the spliceosome.
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: T.el4h RNA
B: Sense Target DNA
C: Maturase reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,40836
Polymers359,6073
Non-polymers80133
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain T.el4h RNA


Mass: 280508.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Production host: Escherichia coli (E. coli)
#2: DNA chain Sense Target DNA


Mass: 14032.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermosynechococcus elongatus (bacteria)
#3: Protein Maturase reverse transcriptase


Mass: 65065.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: tll0114 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DMK2
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: T.el4h group II intron retroelement / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermosynechococcus elongatus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3211refinement
PHENIX1.14_3211refinement
EM software
IDNameCategory
4GctfCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73144 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4R0D

4r0d


Accession code: 4R0D / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009623748
ELECTRON MICROSCOPYf_angle_d1.154136292
ELECTRON MICROSCOPYf_chiral_restr0.05484708
ELECTRON MICROSCOPYf_plane_restr0.0071430
ELECTRON MICROSCOPYf_dihedral_angle_d16.926312195

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