1N36 | pdb_00001n36

Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position

PDB DOI: https://doi.org/10.2210/pdb1N36/pdb
NAKB: 1N36

Classification: RIBOSOME
Organism(s): Thermus thermophilus
Mutation(s): No

Deposited: 2002-10-25 Released: 2002-11-29
Deposition Author(s): Ogle, J.M., Murphy IV, F.V., Tarry, M.J., Ramakrishnan, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.65 Å
R-Value Free:
0.324 (Depositor), 0.368 (DCC)
R-Value Work:
0.260 (Depositor)
R-Value Observed:
0.261 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form

Ogle, J.M., Murphy IV, F.V., Tarry, M.J., Ramakrishnan, V.

(2002) Cell 111: 721-732

PubMed: 12464183 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(02)01086-3
Primary Citation Related Structures:
1N32, 1N33, 1N34, 1N36

PubMed Abstract:
A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.

Organizational Affiliation

MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom.

Macromolecule Content

Total Structure Weight: 782.63 kDa
Atom Count: 51,680
Modeled Residue Count: 3,902
Deposited Residue Count: 4,054
Unique protein chains: 20
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 S2	B	256	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371 Go to UniProtKB: P80371
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80371
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S3	C	239	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372 Go to UniProtKB: P80372
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80372
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S4	D	208	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373 Go to UniProtKB: P80373
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80373
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S5	E	161	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5 Go to UniProtKB: Q5SHQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHQ5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S6	F	101	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8 Go to UniProtKB: Q5SLP8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLP8
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S7	G	155	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291 Go to UniProtKB: P17291
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17291
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S8	H	138	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9 Go to UniProtKB: P0DOY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY9
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S9	I	128	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374 Go to UniProtKB: P80374
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80374
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S10	J	104	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7 Go to UniProtKB: Q5SHN7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHN7
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S11	K	129	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376 Go to UniProtKB: P80376
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80376
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S12	L	135	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3 Go to UniProtKB: Q5SHN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHN3
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S13	M	126	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377 Go to UniProtKB: P80377
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80377
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S14	N	60	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6 Go to UniProtKB: P0DOY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY6
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	O	88	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76 Go to UniProtKB: Q5SJ76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJ76
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S16	P	88	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3 Go to UniProtKB: Q5SJH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJH3
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S17	Q	104	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7 Go to UniProtKB: P0DOY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY7
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S18	R	88	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0 Go to UniProtKB: Q5SLQ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLQ0
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S19	S	92	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2 Go to UniProtKB: Q5SHP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHP2
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S20	T	106	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380 Go to UniProtKB: P80380
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80380
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN THX	U [auth V]	26	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3 Go to UniProtKB: Q5SIH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIH3
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Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
16S RIBOSOMAL RNA	A	1,522	Thermus thermophilus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth N] SDF format, chain V [auth D] MOL2 format, chain W [auth N] MOL2 format, chain V [auth D] mmCIF format, chain W [auth N] mmCIF format, chain V [auth D]	V [auth D], W [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Focus chain W [auth N] Interactions & Density Focus chain V [auth D] Focus chain W [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.65 Å
R-Value Free: 0.324 (Depositor), 0.368 (DCC)
R-Value Work: 0.260 (Depositor)
R-Value Observed: 0.261 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 402.836	α = 90
b = 402.836	β = 90
c = 174.275	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-11-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-11-29
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

1N36 | pdb_00001n36

Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position

Literature

Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form

Biological Assembly 1

Macromolecules

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

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Entity ID: 5

UniProt

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Entity ID: 6

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Entity ID: 7

UniProt

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Entity ID: 8

UniProt

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Entity ID: 9

UniProt

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Sequence Annotations

Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Sequence Annotations

Entity ID: 12

UniProt

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Sequence Annotations

Entity ID: 13

UniProt

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Entity ID: 14

UniProt

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Entity ID: 15

UniProt

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Entity ID: 16

UniProt

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19

UniProt

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Entity ID: 20

UniProt