1F7Y

THE CRYSTAL STRUCTURE OF TWO UUCG LOOPS HIGHLIGHTS THE ROLE PLAYED BY 2'-HYDROXYL GROUPS IN ITS UNUSUAL STABILITY

PDB DOI: https://doi.org/10.2210/pdb1F7Y/pdb
NAKB: 1F7Y

Classification: RIBOSOME
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2000-06-28 Released: 2000-11-22
Deposition Author(s): Ennifar, E., Nikouline, A., Serganov, A., Tishchenko, S., Nevskaya, N., Garber, M., Ehresmann, B., Ehresmann, C., Nikonov, S., Dumas, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.289
R-Value Work: 0.222
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The crystal structure of UUCG tetraloop.

Ennifar, E., Nikulin, A., Tishchenko, S., Serganov, A., Nevskaya, N., Garber, M., Ehresmann, B., Ehresmann, C., Nikonov, S., Dumas, P.

(2000) J Mol Biol 304: 35-42

PubMed: 11071808 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.2000.4204
Primary Citation of Related Structures:
1F7Y

PubMed Abstract:
All large structured RNAs contain hairpin motifs made of a stem closed by several looped nucleotides. The most frequent loop motif is the UUCG one. This motif belongs to the tetraloop family and has the peculiarity of being highly thermodynamically stable. Here, we report the first crystal structure of two UUCG tetraloops embedded in a larger RNA-protein complex solved at 2.8 A resolution. The two loops present in the asymmetric unit are in a different crystal packing environment but, nevertheless, have an identical conformation. The observed structure is globally close to that obtained in solution by nuclear magnetic resonance. However, subtle differences point to a more detailed picture of the role played by 2'-hydroxyl groups in stabilising this tetraloop.

Organizational Affiliation

UPR 9002 du CNRS, IBMC, 15 rue R. Descartes, 67084 Strasbourg-cedex, France.

Macromolecule Content

Total Structure Weight: 29.61 kDa
Atom Count: 2,048
Modelled Residue Count: 143
Deposited Residue Count: 146
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	B [auth A]	89	Thermus thermophilus	Mutation(s): 4
UniProt
Find proteins for P80378 (Thermus thermophilus) Explore P80378 Go to UniProtKB: P80378
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80378
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S RIBOSOMAL RNA FRAGMENT	A [auth B]	57	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain N [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain G [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	L [auth B], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	B [auth A]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.289
R-Value Work: 0.222
R-Value Observed: 0.222
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.8	α = 90
b = 128.8	β = 90
c = 65.1	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-11-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-11-22
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-12-28
Changes: Advisory
Version 1.4: 2021-11-03
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary