7UIM

CryoEM Structure of an Group II Intron Retroelement (apo-complex)

PDB DOI: https://doi.org/10.2210/pdb7UIM/pdb
EM Map EMD-26549: EMDB EMDataResource
NAKB: 7UIM

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Agathobacter rectalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-29 Released: 2022-11-23
Deposition Author(s): Chung, K., Xu, L.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structures of a mobile intron retroelement poised to attack its structured DNA target

Chung, K., Xu, L., Chai, P., Peng, J., Devarkar, S.C., Pyle, A.M.

(2022) Science 378: 627-634

PubMed: 36356138 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.abq2844
Primary Citation of Related Structures:
7UIM, 7UIN

PubMed Abstract:
Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam the genome, integrating by reversal of forward splicing. Here we show that retrotransposition is achieved by a tertiary complex between a structurally elaborate ribozyme, its protein mobility factor, and a structured DNA substrate. We solved cryo-electron microscopy structures of an intact group IIC intron-maturase retroelement that was poised for integration into a DNA stem-loop motif. By visualizing the RNP before and after DNA targeting, we show that it is primed for attack and fits perfectly with its DNA target. This study reveals design principles of a prototypical retroelement and reinforces the hypothesis that group II introns are ancient elements of genetic diversification.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.

Macromolecule Content

Total Structure Weight: 256.22 kDa
Atom Count: 14,772
Modelled Residue Count: 928
Deposited Residue Count: 1,065
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Group II intron reverse transcriptase/maturase	B [auth D]	427	Agathobacter rectalis	Mutation(s): 0 Gene Names: ltrA_2, ltrA, ERS852417_00966, FYL37_05080 EC: 2.7.7.49
UniProt
Find proteins for A0A173ZME3 (Agathobacter rectalis) Explore A0A173ZME3 Go to UniProtKB: A0A173ZME3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A173ZME3
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
E.r IIC Intron	A [auth B]	638	Agathobacter rectalis
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
NH4 (Subject of Investigation/LOI) Query on NH4 Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	P [auth B], Q [auth B]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B]