6Q97

Structure of tmRNA SmpB bound in A site of E. coli 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

How a circularized tmRNA moves through the ribosome.

Rae, C.D.Gordiyenko, Y.Ramakrishnan, V.

(2019) Science 363: 740-744


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SsrA-binding protein
5
145Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: smpB (smqB)
Find proteins for P0A832 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A832
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Nascent peptide
6
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
270Escherichia coli 907713Mutation(s): 0 
Gene Names: rplB
Find proteins for V0A5J4 (Escherichia coli 907713)
Go to UniProtKB:  V0A5J4
Entity ID: 9
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: 10
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: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
175Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 13
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: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
H
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
141Salmonella enterica subsp. indicaMutation(s): 0 
Gene Names: rplM
Find proteins for A0A379XJZ2 (Salmonella enterica subsp. indica)
Go to UniProtKB:  A0A379XJZ2
Entity ID: 17
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: 18
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: 19
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: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
119Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 24
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: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
108Escherichia coli MS 198-1Mutation(s): 0 
Gene Names: rplV
Find proteins for D7X2Z6 (Escherichia coli MS 198-1)
Go to UniProtKB:  D7X2Z6
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 28
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: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
76Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
58Escherichia coli O78:H11 (strain H10407 / ETEC)Mutation(s): 0 
Gene Names: rpmC
Find proteins for E3PKZ6 (Escherichia coli O78:H11 (strain H10407 / ETEC))
Go to UniProtKB:  E3PKZ6
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
56Escherichia coli O104:H4 (strain 2011C-3493)Mutation(s): 0 
Gene Names: rpmD
Find proteins for A0A0E0XV41 (Escherichia coli O104:H4 (strain 2011C-3493))
Go to UniProtKB:  A0A0E0XV41
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
a
66Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
54Escherichia coli MS 198-1Mutation(s): 0 
Gene Names: rpmF
Find proteins for D7XAL4 (Escherichia coli MS 198-1)
Go to UniProtKB:  D7XAL4
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
52Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 36
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: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
37N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
g
225Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
h
208Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
i
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
j
156Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
k
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
l
151Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
m
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
n
126Escherichia coli 2-005-03_S4_C3Mutation(s): 0 
Gene Names: rpsI
Find proteins for A0A029HJ91 (Escherichia coli 2-005-03_S4_C3)
Go to UniProtKB:  A0A029HJ91
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
o
99Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
p
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
q
123Shigella flexneri VA-6Mutation(s): 0 
Gene Names: rpsL
Find proteins for F5NAB8 (Shigella flexneri VA-6)
Go to UniProtKB:  F5NAB8
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
r
115Escherichia coli DEC1CMutation(s): 0 
Gene Names: rpsM
Find proteins for H4IXV7 (Escherichia coli DEC1C)
Go to UniProtKB:  H4IXV7
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
s
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
t
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
u
81Escherichia sp. KTE114Mutation(s): 0 
Gene Names: rpsP
Find proteins for S0UHH0 (Escherichia sp. KTE114)
Go to UniProtKB:  S0UHH0
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
v
80Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
w
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
x
82Escherichia coli 907713Mutation(s): 0 
Gene Names: rpsS
Find proteins for U9ZUL7 (Escherichia coli 907713)
Go to UniProtKB:  U9ZUL7
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
y
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
z
70Escherichia 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 RNA12903Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21534Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli
Entity ID: 6
MoleculeChainsLengthOrganism
tRNA-Met877Escherichia coli
Entity ID: 7
MoleculeChainsLengthOrganism
mRNA96Escherichia coli
Entity ID: 59
MoleculeChainsLengthOrganism
transfer-messenger RNA (tmRNA)4363Escherichia coli
Entity ID: 60
MoleculeChainsLengthOrganism
tRNA-Val777Escherichia coli
Small Molecules
Ligands 2 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
MG
Query on MG

Download SDF File 
Download CCD File 
1, 2, 3, 7, 8, M, Q, X, y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  17 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1, 2
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
OMC
Query on OMC
1
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
2
RNA LINKINGC12 H18 N5 O7 PA
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
7MG
Query on 7MG
2
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
1
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
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
1
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-12-17 
  • Released Date: 2019-03-13 
  • Deposition Author(s): Rae, C.D.

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

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release