1DK1 | pdb_00001dk1

DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1DK1/pdb
NAKB: 1DK1

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

Deposited: 1999-12-06 Released: 2000-04-02
Deposition Author(s): Nikulin, A., Serganov, A., Ennifar, E., Tischenko, S., Nevskaya, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.291 (Depositor)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of the S15-rRNA complex.

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

(2000) Nat Struct Biol 7: 273-277

PubMed: 10742169 Search on PubMed
DOI: https://doi.org/10.1038/74028
Primary Citation Related Structures:
1DK1

PubMed Abstract:
In bacterial ribosomes, the small (30S) ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 is of particular interest because it binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. Here we report the 2.8 ¿ resolution crystal structure of the highly conserved S15-rRNA complex. Protein S15 interacts in the minor groove with a G-U/G-C motif and a three-way junction. The latter is constrained by a conserved base triple and stacking interactions, and locked into place by magnesium ions and protein side chains, mainly through interactions with the unique three-dimensional geometry of the backbone. The present structure gives insights into the dual role of S15 in ribosome assembly and translational regulation.

Organizational Affiliation

Institute of Protein Research, Pushchino, Moscow Region, 142292, Russia.

Macromolecule Content

Total Structure Weight: 29.27 kDa
Atom Count: 2,047
Modeled Residue Count: 143
Deposited Residue Count: 143
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	B [auth A]	86	Thermus thermophilus	Mutation(s): 4
UniProt
Find proteins for P80378 (Thermus thermophilus) Explore P80378 Go to UniProtKB: P80378
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80378
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RRNA FRAGMENT	A [auth B]	57	Thermus thermophilus
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 G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [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 G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [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 G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [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: 0.291 (Depositor)
R-Value Work: 0.213 (Depositor)
R-Value Observed: 0.213 (Depositor)

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: 2000-04-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-04-02
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: 2018-01-31
Changes: Experimental preparation
Version 1.5: 2021-11-03
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-10-30
Changes: Data collection, Structure summary