1JGQ

The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGQ, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The path of messenger RNA through the ribosome.

Yusupova, G.Z.Yusupov, M.M.Cate, J.H.Noller, H.F.

(2001) Cell 106: 233-241

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-D ...

    Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (-1 to +7), centered on the junction between the A and P codons, are exposed, and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting.


    Organizational Affiliation

    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
E
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
F
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
G
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
H
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
I
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
J
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
K
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
L
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
M
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
N
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
O
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
P
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
Q
61Thermus aquaticusMutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
R
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
S
91Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
T
105Thermus aquaticusMutation(s): 0 
Gene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
U
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
V
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
W
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
X
26Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 1
MoleculeChainsLengthOrganism
30S 16S ribosomal RNAA1522Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
tRNA(Phe)B,C76N/A
Entity ID: 3
MoleculeChainsLengthOrganism
tRNA(Phe)D74N/A
Entity ID: 4
MoleculeChainsLengthOrganism
MESSENGER RNA MF36136N/A
Small Molecules
Modified Residues  12 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
B, C, D
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
B, C, D
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
B, C
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
B, C
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
B, C
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
D
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
B, C
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
B, C
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
B, C
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
B, C
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
B, C, D
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
B, C, D
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 507.200α = 90.00
b = 507.200β = 90.00
c = 803.660γ = 90.00
Software Package:
Software NamePurpose
Omodel building
DENZOdata reduction
CCP4model building
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-02-14
    Type: Experimental preparation