8HD7

The intermediate pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside

PDB DOI: https://doi.org/10.2210/pdb8HD7/pdb
NAKB: 8HD7
EM Map EMD-34671: EMDB EMDataResource

Classification: RNA
Organism(s): Tetrahymena thermophila
Expression System: synthetic construct
Mutation(s): Yes

Deposited: 2022-11-03 Released: 2023-03-29
Deposition Author(s): Luo, B., Zhang, C., Ling, X., Mukherjee, S., Jia, G., Xie, J., Jia, X., Liu, L., Baulin, E.F., Luo, Y., Jiang, L., Dong, H., Wei, X., Bujnicki, J.M., Su, Z.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), Polish National Science Centre, European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.52 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

Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing

Luo, B., Zhang, C., Ling, X., Mukherjee, S., Jia, G., Xie, J., Jia, X., Liu, L., Baulin, E.F., Luo, Y., Jiang, L., Dong, H., Wei, X., Bujnicki, J.M., Su, Z.

(2023) Nat Catal

DOI: https://doi.org/10.1038/s41929-023-00934-3

Macromolecule Content

Total Structure Weight: 135.96 kDa
Atom Count: 8,983
Modelled Residue Count: 419
Deposited Residue Count: 419
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
The intermediate pre-Tet-S1 state molecule of co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside	A [auth N]	419	Tetrahymena thermophila
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPD Query on SPD Download Ideal Coordinates CCD File SDF format, chain B [auth N] MOL2 format, chain B [auth N]	B [auth N]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain B [auth N] Interactions & Density Focus chain B [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain BA [auth N] SDF format, chain C [auth N] SDF format, chain CA [auth N] SDF format, chain D [auth N] SDF format, chain E [auth N] SDF format, chain F [auth N] SDF format, chain G [auth N] SDF format, chain H [auth N] SDF format, chain I [auth N] SDF format, chain J [auth N] SDF format, chain K [auth N] SDF format, chain L [auth N] SDF format, chain M [auth N] SDF format, chain N SDF format, chain O [auth N] SDF format, chain P [auth N] SDF format, chain Q [auth N] SDF format, chain R [auth N] SDF format, chain S [auth N] SDF format, chain T [auth N] SDF format, chain U [auth N] SDF format, chain V [auth N] SDF format, chain W [auth N] SDF format, chain X [auth N] SDF format, chain Y [auth N] SDF format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain BA [auth N] MOL2 format, chain C [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain D [auth N] MOL2 format, chain E [auth N] MOL2 format, chain F [auth N] MOL2 format, chain G [auth N] MOL2 format, chain H [auth N] MOL2 format, chain I [auth N] MOL2 format, chain J [auth N] MOL2 format, chain K [auth N] MOL2 format, chain L [auth N] MOL2 format, chain M [auth N] MOL2 format, chain N MOL2 format, chain O [auth N] MOL2 format, chain P [auth N] MOL2 format, chain Q [auth N] MOL2 format, chain R [auth N] MOL2 format, chain S [auth N] MOL2 format, chain T [auth N] MOL2 format, chain U [auth N] MOL2 format, chain V [auth N] MOL2 format, chain W [auth N] MOL2 format, chain X [auth N] MOL2 format, chain Y [auth N] MOL2 format, chain Z [auth N]	AA [auth N] BA [auth N] C [auth N] CA [auth N] D [auth N] AA [auth N], BA [auth N], C [auth N], CA [auth N], D [auth N], E [auth N], F [auth N], G [auth N], H [auth N], I [auth N], J [auth N], K [auth N], L [auth N], M [auth N], N, O [auth N], P [auth N], Q [auth N], R [auth N], S [auth N], T [auth N], U [auth N], V [auth N], W [auth N], X [auth N], Y [auth N], Z [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain BA [auth N] Focus chain C [auth N] Focus chain CA [auth N] Focus chain D [auth N] Focus chain E [auth N] Focus chain F [auth N] Focus chain G [auth N] Focus chain H [auth N] Focus chain I [auth N] Focus chain J [auth N] Focus chain K [auth N] Focus chain L [auth N] Focus chain M [auth N] Focus chain N Focus chain O [auth N] Focus chain P [auth N] Focus chain Q [auth N] Focus chain R [auth N] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N] Focus chain X [auth N] Focus chain Y [auth N] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain BA [auth N] Focus chain C [auth N] Focus chain CA [auth N] Focus chain D [auth N] Focus chain E [auth N] Focus chain F [auth N] Focus chain G [auth N] Focus chain H [auth N] Focus chain I [auth N] Focus chain J [auth N] Focus chain K [auth N] Focus chain L [auth N] Focus chain M [auth N] Focus chain N Focus chain O [auth N] Focus chain P [auth N] Focus chain Q [auth N] Focus chain R [auth N] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N] Focus chain X [auth N] Focus chain Y [auth N] Focus chain Z [auth N]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.52 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.15
MODEL REFINEMENT	Coot	0.8.7
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA1301900
Ministry of Science and Technology (MoST, China)	China	2022YFC2303700
National Natural Science Foundation of China (NSFC)	China	32222040
National Natural Science Foundation of China (NSFC)	China	32070049
Polish National Science Centre	Poland	2017/26/A/NZ1/01083
Polish National Science Centre	Poland	2021/43/D/NZ1/03360
European Molecular Biology Organization (EMBO)	European Union	ALTF 525-2022