7XD6

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


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 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7EZ0


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 


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
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]434Tetrahymena thermophila
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
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]25Tetrahymena thermophila
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

Download Ideal Coordinates CCD File 
EA [auth N]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTCoot0.9.1
MODEL REFINEMENTPHENIX1.15

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFA1301900
Ministry of Science and Technology (MoST, China)China2022YFC2303700
National Natural Science Foundation of China (NSFC)China32222040
National Natural Science Foundation of China (NSFC)China32070049
Polish National Science CentrePoland2017/26/A/NZ1/01083
Polish National Science CentrePoland2021/43/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