4V8C

Crystal structure analysis of ribosomal decoding (near-cognate tRNA-leu complex with paromomycin).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new understanding of the decoding principle on the ribosome.

Demeshkina, N.Jenner, L.Westhof, E.Yusupov, M.Yusupova, G.

(2012) Nature 484: 256-259

  • DOI: 10.1038/nature10913
  • Primary Citation of Related Structures:  3TVE, 3TVF, 3TVG, 3TVH, 3UYD, 3UYE, 3UYF, 3UYG, 3UZ1, 3UZ2, 3UZ3, 3UZ4, 3UZ6, 3UZ7, 3UZ8, 3UZ9, 3UZF, 3UZG, 3UZH, 3UZI, 3UZK, 3UZL, 3UZM, 3UZN, 4V87, 4V8B, 4V8D, 4V8E, 4V8F

  • PubMed Abstract: 
  • During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA ...

    During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site, actively monitor cognate tRNA, and that recognition of the correct codon-anticodon duplex induces an overall ribosome conformational change (domain closure). Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1-3.4 Å resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson-Crick base pairs. When U·G and G·U mismatches, generally considered to form wobble base pairs, are at the first or second codon-anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C·G pair. This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.


    Organizational Affiliation

    Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AD, BD
276Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AE, BE
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AF, BF
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AG, BG
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AH, BH
180Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplF
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY8
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
AK, BK
148Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AM, BM
140Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AN, BN
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AO, BO
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AP, BP
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
A0, B0
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AQ, BQ
112Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AR, BR
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
A1, B1
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
A2, B2
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AS, BS
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AT, BT
96Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AU, BU
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AV, BV
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
A3, B3
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
AZ, BZ
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AW, BW
72Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP6
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AX, BX
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
A4, B4
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
A5, B5
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A6, B6
54Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A7, B7
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
A8, B8
65Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
CE, DE
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
CF, DF
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
CG, DG
208Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
CH, DH
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
CI, DI
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
CJ, DJ
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
CK, DK
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
CL, DL
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
CM, DM
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
CN, DN
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
CO, DO
132Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
CP, DP
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
CQ, DQ
61Thermus aquaticusGene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
CR, DR
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
CS, DS
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
CT, DT
105Thermus aquaticusGene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
CU, DU
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
CV, DV
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
CW, DW
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
CX, DX
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (2912-MER)AA,BA2912Thermus thermophilus HB8
Entity ID: 2
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNAAB,BB122Thermus thermophilus HB8
Entity ID: 31
MoleculeChainsLengthOrganism
16S ribosomal RNACA,DA1506Thermus thermophilus HB8
Entity ID: 52
MoleculeChainsLengthOrganism
TRNA-LEUCB,DB87N/A
Entity ID: 53
MoleculeChainsLengthOrganism
TRNA-FMETCC,CD,DC,DD77Escherichia coli str. K-12 substr. MDS42
Entity ID: 54
MoleculeChainsLengthOrganism
MRNAC1,D110N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
CG, CQ, DG, DQ
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PAR
Query on PAR

Download SDF File 
Download CCD File 
CA, DA
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A0, A1, A2, A3, A5, A6, A7, AA, AB, AD, AE, AF, AO, AU, AZ, B1, B3, B5, BA, BB, BD, BE, BP, BR, C1, CA, CB, CC, CD, CG, CN, CQ, CT, DA, DB, DC, DG, DH, DS
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 209.430α = 90.00
b = 448.150β = 90.00
c = 619.400γ = 90.00
Software Package:
Software NamePurpose
RemDAqdata collection
PHENIXphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
PHENIXmodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2017-11-22
    Type: Advisory, Refinement description