7XD6 | pdb_00007xd6

The Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon

PDB DOI: https://doi.org/10.2210/pdb7XD6/pdb
EM Map EMD-33137: EMDB EMDataResource
NAKB: 7XD6

Classification: RNA
Organism(s): Tetrahymena thermophila
Expression System: synthetic construct
Mutation(s): No

Deposited: 2022-03-26 Released: 2023-04-05
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: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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: 148.91 kDa
Atom Count: 9,843
Modeled Residue Count: 459
Deposited Residue Count: 459
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)	A [auth N]	434	Tetrahymena thermophila
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)	B [auth A]	25	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 EA [auth N] MOL2 format, chain EA [auth N] mmCIF format, chain EA [auth N]	EA [auth N]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain EA [auth N] Interactions & Density Focus chain EA [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth N] SDF format, chain Y [auth N] SDF format, chain X [auth N] SDF format, chain W [auth N] SDF format, chain V [auth N] SDF format, chain U [auth N] SDF format, chain T [auth N] SDF format, chain S [auth N] SDF format, chain R [auth N] SDF format, chain Q [auth N] SDF format, chain P [auth N] SDF format, chain O [auth N] SDF format, chain N SDF format, chain M [auth N] SDF format, chain L [auth N] SDF format, chain K [auth N] SDF format, chain J [auth N] SDF format, chain I [auth N] SDF format, chain H [auth N] SDF format, chain G [auth N] SDF format, chain F [auth N] SDF format, chain E [auth N] SDF format, chain DA [auth N] SDF format, chain D [auth N] SDF format, chain CA [auth N] SDF format, chain C [auth N] SDF format, chain BA [auth N] SDF format, chain AA [auth N] MOL2 format, chain Z [auth N] MOL2 format, chain Y [auth N] MOL2 format, chain X [auth N] MOL2 format, chain W [auth N] MOL2 format, chain V [auth N] MOL2 format, chain U [auth N] MOL2 format, chain T [auth N] MOL2 format, chain S [auth N] MOL2 format, chain R [auth N] MOL2 format, chain Q [auth N] MOL2 format, chain P [auth N] MOL2 format, chain O [auth N] MOL2 format, chain N MOL2 format, chain M [auth N] MOL2 format, chain L [auth N] MOL2 format, chain K [auth N] MOL2 format, chain J [auth N] MOL2 format, chain I [auth N] MOL2 format, chain H [auth N] MOL2 format, chain G [auth N] MOL2 format, chain F [auth N] MOL2 format, chain E [auth N] MOL2 format, chain DA [auth N] MOL2 format, chain D [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain C [auth N] MOL2 format, chain BA [auth N] MOL2 format, chain AA [auth N] mmCIF format, chain Z [auth N] mmCIF format, chain Y [auth N] mmCIF format, chain X [auth N] mmCIF format, chain W [auth N] mmCIF format, chain V [auth N] mmCIF format, chain U [auth N] mmCIF format, chain T [auth N] mmCIF format, chain S [auth N] mmCIF format, chain R [auth N] mmCIF format, chain Q [auth N] mmCIF format, chain P [auth N] mmCIF format, chain O [auth N] mmCIF format, chain N mmCIF format, chain M [auth N] mmCIF format, chain L [auth N] mmCIF format, chain K [auth N] mmCIF format, chain J [auth N] mmCIF format, chain I [auth N] mmCIF format, chain H [auth N] mmCIF format, chain G [auth N] mmCIF format, chain F [auth N] mmCIF format, chain E [auth N] mmCIF format, chain DA [auth N] mmCIF format, chain D [auth N] mmCIF format, chain CA [auth N] mmCIF format, chain C [auth N] mmCIF format, chain BA [auth N] mmCIF format, chain AA [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], DA [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 DA [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 DA [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: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	Coot	0.9.1
MODEL REFINEMENT	PHENIX	1.15

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-05

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	--

Revision History (Full details and data files)

Version 1.0: 2023-04-05
Type: Initial release
Version 1.1: 2024-06-26
Changes: Data collection, Refinement description
Version 1.2: 2025-03-12
Changes: Data collection, Database references, Structure summary