7XD4

The intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 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 


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exonA [auth N]423Tetrahymena thermophila
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth N]
B [auth N]
BA [auth N]
C [auth N]
CA [auth N]
AA [auth N],
B [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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.15
MODEL REFINEMENTCoot0.8.7

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)China32070049
National Natural Science Foundation of China (NSFC)China32222040
Polish National Science CentrePoland2017/26/A/NZ1/01083
Polish National Science CentrePoland2021/43/D/NZ1/03360
European Molecular Biology Organization (EMBO)European UnionALTF 525-2022

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection, Refinement description