9CBX

Tetrahymena ribozyme with automatically identified water and magnesium ions

PDB DOI: https://doi.org/10.2210/pdb9CBX/pdb
EM Map EMD-42499: EMDB EMDataResource

Classification: RNA
Organism(s): Tetrahymena thermophila
Mutation(s): No

Deposited: 2024-06-20 Released: 2024-11-20
Deposition Author(s): Kretsch, R.C., Li, S., Pintilie, G., Palo, M.Z., Case, D.A., Das, R., Zhang, K., Chiu, W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), Chinese Academy of Sciences, Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Complex Water Networks Visualized through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of RNA

Kretsch, R.C., Li, S., Pintilie, G., Palo, M.Z., Case, D.A., Das, R., Zhang, K., Chiu, W.

To be published.

Macromolecule Content

Total Structure Weight: 126.41 kDa
Atom Count: 8,617
Modelled Residue Count: 387
Deposited Residue Count: 387
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (387-MER)	A [auth N]	387	Tetrahymena thermophila
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N SDF format, chain R [auth N] SDF format, chain Z [auth N] SDF format, chain AA [auth N] SDF format, chain AB [auth N] SDF format, chain B [auth N] SDF format, chain BA [auth N] SDF format, chain BB [auth N] SDF format, chain C [auth N] SDF format, chain CA [auth N] SDF format, chain CB [auth N] SDF format, chain D [auth N] SDF format, chain DA [auth N] SDF format, chain E [auth N] SDF format, chain EA [auth N] SDF format, chain F [auth N] SDF format, chain FA [auth N] SDF format, chain G [auth N] SDF format, chain GA [auth N] SDF format, chain H [auth N] SDF format, chain HA [auth N] SDF format, chain I [auth N] SDF format, chain IA [auth N] SDF format, chain J [auth N] SDF format, chain JA [auth N] SDF format, chain K [auth N] SDF format, chain KA [auth N] SDF format, chain L [auth N] SDF format, chain LA [auth N] SDF format, chain M [auth N] SDF format, chain MA [auth N] SDF format, chain NA [auth N] SDF format, chain O [auth N] SDF format, chain OA [auth N] SDF format, chain P [auth N] SDF format, chain PA [auth N] SDF format, chain Q [auth N] SDF format, chain QA [auth N] SDF format, chain RA [auth N] SDF format, chain S [auth N] SDF format, chain SA [auth N] SDF format, chain T [auth N] SDF format, chain TA [auth N] SDF format, chain U [auth N] SDF format, chain UA [auth N] SDF format, chain V [auth N] SDF format, chain VA [auth N] SDF format, chain W [auth N] SDF format, chain WA [auth N] SDF format, chain X [auth N] SDF format, chain XA [auth N] SDF format, chain Y [auth N] SDF format, chain YA [auth N] SDF format, chain ZA [auth N] MOL2 format, chain N MOL2 format, chain R [auth N] MOL2 format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain AB [auth N] MOL2 format, chain B [auth N] MOL2 format, chain BA [auth N] MOL2 format, chain BB [auth N] MOL2 format, chain C [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain CB [auth N] MOL2 format, chain D [auth N] MOL2 format, chain DA [auth N] MOL2 format, chain E [auth N] MOL2 format, chain EA [auth N] MOL2 format, chain F [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain G [auth N] MOL2 format, chain GA [auth N] MOL2 format, chain H [auth N] MOL2 format, chain HA [auth N] MOL2 format, chain I [auth N] MOL2 format, chain IA [auth N] MOL2 format, chain J [auth N] MOL2 format, chain JA [auth N] MOL2 format, chain K [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain L [auth N] MOL2 format, chain LA [auth N] MOL2 format, chain M [auth N] MOL2 format, chain MA [auth N] MOL2 format, chain NA [auth N] MOL2 format, chain O [auth N] MOL2 format, chain OA [auth N] MOL2 format, chain P [auth N] MOL2 format, chain PA [auth N] MOL2 format, chain Q [auth N] MOL2 format, chain QA [auth N] MOL2 format, chain RA [auth N] MOL2 format, chain S [auth N] MOL2 format, chain SA [auth N] MOL2 format, chain T [auth N] MOL2 format, chain TA [auth N] MOL2 format, chain U [auth N] MOL2 format, chain UA [auth N] MOL2 format, chain V [auth N] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth N] MOL2 format, chain WA [auth N] MOL2 format, chain X [auth N] MOL2 format, chain XA [auth N] MOL2 format, chain Y [auth N] MOL2 format, chain YA [auth N] MOL2 format, chain ZA [auth N] mmCIF format, chain N mmCIF format, chain R [auth N] mmCIF format, chain Z [auth N] mmCIF format, chain AA [auth N] mmCIF format, chain AB [auth N] mmCIF format, chain B [auth N] mmCIF format, chain BA [auth N] mmCIF format, chain BB [auth N] mmCIF format, chain C [auth N] mmCIF format, chain CA [auth N] mmCIF format, chain CB [auth N] mmCIF format, chain D [auth N] mmCIF format, chain DA [auth N] mmCIF format, chain E [auth N] mmCIF format, chain EA [auth N] mmCIF format, chain F [auth N] mmCIF format, chain FA [auth N] mmCIF format, chain G [auth N] mmCIF format, chain GA [auth N] mmCIF format, chain H [auth N] mmCIF format, chain HA [auth N] mmCIF format, chain I [auth N] mmCIF format, chain IA [auth N] mmCIF format, chain J [auth N] mmCIF format, chain JA [auth N] mmCIF format, chain K [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain L [auth N] mmCIF format, chain LA [auth N] mmCIF format, chain M [auth N] mmCIF format, chain MA [auth N] mmCIF format, chain NA [auth N] mmCIF format, chain O [auth N] mmCIF format, chain OA [auth N] mmCIF format, chain P [auth N] mmCIF format, chain PA [auth N] mmCIF format, chain Q [auth N] mmCIF format, chain QA [auth N] mmCIF format, chain RA [auth N] mmCIF format, chain S [auth N] mmCIF format, chain SA [auth N] mmCIF format, chain T [auth N] mmCIF format, chain TA [auth N] mmCIF format, chain U [auth N] mmCIF format, chain UA [auth N] mmCIF format, chain V [auth N] mmCIF format, chain VA [auth N] mmCIF format, chain W [auth N] mmCIF format, chain WA [auth N] mmCIF format, chain X [auth N] mmCIF format, chain XA [auth N] mmCIF format, chain Y [auth N] mmCIF format, chain YA [auth N] mmCIF format, chain ZA [auth N]	AA [auth N] AB [auth N] B [auth N] BA [auth N] BB [auth N] AA [auth N], AB [auth N], B [auth N], BA [auth N], BB [auth N], C [auth N], CA [auth N], CB [auth N], D [auth N], DA [auth N], E [auth N], EA [auth N], F [auth N], FA [auth N], G [auth N], GA [auth N], H [auth N], HA [auth N], I [auth N], IA [auth N], J [auth N], JA [auth N], K [auth N], KA [auth N], L [auth N], LA [auth N], M [auth N], MA [auth N], N, NA [auth N], O [auth N], OA [auth N], P [auth N], PA [auth N], Q [auth N], QA [auth N], R [auth N], RA [auth N], S [auth N], SA [auth N], T [auth N], TA [auth N], U [auth N], UA [auth N], V [auth N], VA [auth N], W [auth N], WA [auth N], X [auth N], XA [auth N], Y [auth N], YA [auth N], Z [auth N], ZA [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain AB [auth N] Focus chain B [auth N] Focus chain BA [auth N] Focus chain BB [auth N] Focus chain C [auth N] Focus chain CA [auth N] Focus chain CB [auth N] Focus chain D [auth N] Focus chain DA [auth N] Focus chain E [auth N] Focus chain EA [auth N] Focus chain F [auth N] Focus chain FA [auth N] Focus chain G [auth N] Focus chain GA [auth N] Focus chain H [auth N] Focus chain HA [auth N] Focus chain I [auth N] Focus chain IA [auth N] Focus chain J [auth N] Focus chain JA [auth N] Focus chain K [auth N] Focus chain KA [auth N] Focus chain L [auth N] Focus chain LA [auth N] Focus chain M [auth N] Focus chain MA [auth N] Focus chain N Focus chain NA [auth N] Focus chain O [auth N] Focus chain OA [auth N] Focus chain P [auth N] Focus chain PA [auth N] Focus chain Q [auth N] Focus chain QA [auth N] Focus chain R [auth N] Focus chain RA [auth N] Focus chain S [auth N] Focus chain SA [auth N] Focus chain T [auth N] Focus chain TA [auth N] Focus chain U [auth N] Focus chain UA [auth N] Focus chain V [auth N] Focus chain VA [auth N] Focus chain W [auth N] Focus chain WA [auth N] Focus chain X [auth N] Focus chain XA [auth N] Focus chain Y [auth N] Focus chain YA [auth N] Focus chain Z [auth N] Focus chain ZA [auth N] Interactions & Density Focus chain AA [auth N] Focus chain AB [auth N] Focus chain B [auth N] Focus chain BA [auth N] Focus chain BB [auth N] Focus chain C [auth N] Focus chain CA [auth N] Focus chain CB [auth N] Focus chain D [auth N] Focus chain DA [auth N] Focus chain E [auth N] Focus chain EA [auth N] Focus chain F [auth N] Focus chain FA [auth N] Focus chain G [auth N] Focus chain GA [auth N] Focus chain H [auth N] Focus chain HA [auth N] Focus chain I [auth N] Focus chain IA [auth N] Focus chain J [auth N] Focus chain JA [auth N] Focus chain K [auth N] Focus chain KA [auth N] Focus chain L [auth N] Focus chain LA [auth N] Focus chain M [auth N] Focus chain MA [auth N] Focus chain N Focus chain NA [auth N] Focus chain O [auth N] Focus chain OA [auth N] Focus chain P [auth N] Focus chain PA [auth N] Focus chain Q [auth N] Focus chain QA [auth N] Focus chain R [auth N] Focus chain RA [auth N] Focus chain S [auth N] Focus chain SA [auth N] Focus chain T [auth N] Focus chain TA [auth N] Focus chain U [auth N] Focus chain UA [auth N] Focus chain V [auth N] Focus chain VA [auth N] Focus chain W [auth N] Focus chain WA [auth N] Focus chain X [auth N] Focus chain XA [auth N] Focus chain Y [auth N] Focus chain YA [auth N] Focus chain Z [auth N] Focus chain ZA [auth N]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	ISOLDE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM122579
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM129541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM079429
Chinese Academy of Sciences	China	XDB0490000
Other government		Center for Advanced Interdisciplinary Science and Biomedicine of IHM QYPY20220019
Other government		National Key R&D Program of China 2022YFC2303700
Other government		National Key R&D Program of China 2022YFA1302700
Other government		Fundamental Research Funds for the Central Universities WK9100000032
Other government		Fundamental Research Funds for the Central Universities WK9100000044