4V4J

Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.83 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.327 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.

Korostelev, A.Trakhanov, S.Asahara, H.Laurberg, M.Lancaster, L.Noller, H.F.

(2007) Proc.Natl.Acad.Sci.Usa 104: 16840-16843

  • DOI: 10.1073/pnas.0707850104
  • Primary Citation of Related Structures:  1VSP, 2QNH

  • PubMed Abstract: 
  • The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were b ...

    The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were biased along its helical axis, suggesting that during the first step of translocation, the SD helix moves along its helical screw axis. Contacts between the SD helix and the ribosome were primarily through interactions with helices 23a, 26, and 28 of 16S rRNA. Contact with the neck (helix 28) of the 30S subunit near its hinge point suggests that formation of the SD helix could affect positioning of the head of the 30S subunit for optimal interaction with initiator tRNA. The bulged U723 in helix 23a interacts with the minor groove of the SD helix at the C1539.G-10 base pair, explaining its selective conservation in bacteria and archaea.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95060, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
A
229Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplA
Find proteins for Q72GV9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GV9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
276Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplB
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplC
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I04
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
205Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplD
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I05
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
182Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplE
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I16
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
180Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplF
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I19
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
148Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplI
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GV5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
H
140Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplM
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
I
122Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplN
Find proteins for Q72I14 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I14
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
J
150Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplO
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I23
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
K
141Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplP
Find proteins for Q72I11 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I11
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
L
118Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplQ
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
M
112Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplR
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I20
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
N
146Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplS
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JU9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
O
118Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplT
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
P
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplU
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
Q
113Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplV
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I09
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
R
96Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplW
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I06
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
S
110Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplX
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I15
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
T
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplY (ctc)
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
U
85Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmA
Find proteins for Q72HR3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR3
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
LSU ribosomal protein L28P
V
98Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmB
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72G84
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
W
72Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmC
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
LSU ribosomal protein L30P
X
60Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmD
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I22
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Y
60Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmF (rpl32)
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62652
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
Z
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: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
a
65Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmI
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L77
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
b
37Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmJ
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I28
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
c
256Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
d
239Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
e
209Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
f
162Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsE (rps5)
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
g
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsF (rps6)
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
h
156Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
i
138Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsH (rps8)
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
j
128Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
k
105Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsJ (rps10)
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
l
129Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
m
132Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsL (rps12)
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
n
126Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
o
61Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsZ (rps14, rpsN)
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
p
89Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsO (rps15)
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
q
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
r
105Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsQ (rps17)
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62658
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
s
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
t
93Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsS (rps19)
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
u
106Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsT (rps20)
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62661
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
v
27Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsU
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62613
Entity ID: 1
MoleculeChainsLengthOrganism
23S LARGE SUBUNIT RIBOSOMAL RNAw2889Thermus thermophilus HB27
Entity ID: 2
MoleculeChainsLengthOrganism
5S LARGE SUBUNIT RIBOSOMAL RNAx120Thermus thermophilus HB27
Entity ID: 31
MoleculeChainsLengthOrganism
16S RNAy1522Thermus thermophilus HB27
Entity ID: 32
MoleculeChainsLengthOrganism
P-site tRNAfMETz77Thermus thermophilus HB27
Entity ID: 33
MoleculeChainsLengthOrganism
E-site tRNA276Thermus thermophilus HB27
Entity ID: 34
MoleculeChainsLengthOrganism
MRNA318Thermus thermophilus HB27
Small Molecules
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
2, y
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
y
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
y
RNA LINKINGC12 H18 N5 O8 PG
MA6
Query on MA6
y
RNA LINKINGC12 H18 N5 O7 PA
2MG
Query on 2MG
y
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
y
RNA LINKINGC11 H18 N5 O8 PG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.83 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.327 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 507.210α = 90.00
b = 507.210β = 90.00
c = 692.510γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CNSrefinement
CNSphasing
ADSCdata collection
d*TREKdata reduction
REFMACrefinement
SCALAdata 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