5MDZ

Structure of the 70S ribosome (empty A site)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Translational termination without a stop codon.

James, N.R.Brown, A.Gordiyenko, Y.Ramakrishnan, V.

(2016) Science 354: 1437-1440

  • DOI: 10.1126/science.aai9127
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine str ...

    Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.


    Organizational Affiliation

    Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
H
165Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
a
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
g
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
h
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
i
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
j
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
k
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
l
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
m
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
n
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
o
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
p
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
q
124Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
r
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
s
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
t
89Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
u
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
v
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
w
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
x
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
y
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
z
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA12904Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21534Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
mRNA418Escherichia coli
Entity ID: 5
MoleculeChainsLengthOrganism
fMet-NH-tRNA(fMet)578Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
a, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FME
Query on FME

Download SDF File 
Download CCD File 
5
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
1, 2, 3, 5, b, f, i, n
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  21 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1, 2, 5
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
1, 2
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
1
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
1
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
1
RNA LINKINGC11 H16 N5 O8 PG
FME
Query on FME
5
L-PEPTIDE LINKINGC6 H11 N O3 SMET
OMC
Query on OMC
1
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
2
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
5
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
1, 2
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
1
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
2
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
1
RNA LINKINGC11 H16 N5 O8 PG
8AN
Query on 8AN
5
RNA LINKINGC10 H15 N6 O6 PA
7MG
Query on 7MG
2
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
1, 5
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
1
RNA LINKINGC11 H16 N5 O7 PA
0TD
Query on 0TD
q
L-PEPTIDE LINKINGC5 H9 N O4 SASP
4OC
Query on 4OC
2, 5
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
1
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
5
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2016-12-28
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Author supporting evidence, Data collection, Derived calculations
  • Version 2.0: 2018-10-03
    Type: Data collection, Derived calculations, Polymer sequence, Refinement description, Structure summary