3U4M | pdb_00003u4m

Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb3U4M/pdb
NAKB: 3U4M

Classification: RNA/RNA BINDING PROTEIN
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-10-10 Released: 2012-08-08
Deposition Author(s): Gabdulkhakov, A.G., Nevskaya, N.A., NIkonov, S.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.208 (Depositor), 0.202 (DCC)
R-Value Work:
0.179 (Depositor), 0.174 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

High-resolution crystal structure of the isolated ribosomal L1 stalk.

Tishchenko, S., Gabdulkhakov, A., Nevskaya, N., Sarskikh, A., Kostareva, O., Nikonova, E., Sycheva, A., Moshkovskii, S., Garber, M., Nikonov, S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1051-1057

PubMed: 22868771 Search on PubMed
DOI: https://doi.org/10.1107/S0907444912020136
Primary Citation Related Structures:
3U4M

PubMed Abstract:
The crystal structure of the isolated full-length ribosomal L1 stalk, consisting of Thermus thermophilus ribosomal protein L1 in complex with a specific 80-nucleotide fragment of 23S rRNA, has been solved for the first time at high resolution. The structure revealed details of protein-RNA interactions in the L1 stalk. Analysis of the crystal packing enabled the identification of sticky sites on the protein and the 23S rRNA which may be important for ribosome assembly and function. The structure was used to model different conformational states of the ribosome. This approach provides an insight into the roles of domain II of L1 and helix 78 of rRNA in ribosome function.

Organizational Affiliation

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation.

Macromolecule Content

Total Structure Weight: 52.06 kDa
Atom Count: 3,763
Modeled Residue Count: 308
Deposited Residue Count: 309
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	A	229	Thermus thermophilus	Mutation(s): 0 Gene Names: rplA, rpl1
UniProt
Find proteins for P27150 (Thermus thermophilus) Explore P27150 Go to UniProtKB: P27150
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27150
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (80-MER)	B	80	Thermus thermophilus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	D [auth A] E [auth A] F [auth A] O [auth B] P [auth B] D [auth A], E [auth A], F [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain G [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	G [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain W [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B]	J [auth A], K [auth A], L [auth A], M [auth A], W [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208 (Depositor), 0.202 (DCC)
R-Value Work: 0.179 (Depositor), 0.174 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.55	α = 90
b = 68.9	β = 90
c = 117.56	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-08

Deposition Author(s):

Gabdulkhakov, A.G.

Nevskaya, N.A.

NIkonov, S.V.

Revision History (Full details and data files)

Version 1.0: 2012-08-08
Type: Initial release
Version 1.1: 2013-01-23
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description