5L3P

Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis.

Arenz, S.Abdelshahid, M.Sohmen, D.Payoe, R.Starosta, A.L.Berninghausen, O.Hauryliuk, V.Beckmann, R.Wilson, D.N.

(2016) Nucleic Acids Res 44: 6471-6481

  • DOI: 10.1093/nar/gkw470
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The signaling molecules (p)ppGpp globally rewire the cel ...

    Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The signaling molecules (p)ppGpp globally rewire the cellular transcriptional program and general metabolism, leading to stress adaptation. Despite the additional importance of the stringent response for regulation of bacterial virulence, antibiotic resistance and persistence, structural insight into how the ribosome and deacylated-tRNA stimulate RelA-mediated (p)ppGpp has been lacking. Here, we present a cryo-EM structure of RelA in complex with the Escherichia coli 70S ribosome with an average resolution of 3.7 Å and local resolution of 4 to >10 Å for RelA. The structure reveals that RelA adopts a unique 'open' conformation, where the C-terminal domain (CTD) is intertwined around an A/T-like tRNA within the intersubunit cavity of the ribosome and the N-terminal domain (NTD) extends into the solvent. We propose that the open conformation of RelA on the ribosome relieves the autoinhibitory effect of the CTD on the NTD, thus leading to stimulation of (p)ppGpp synthesis by RelA.


    Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich 81377, Germany wilson@lmb.uni-muenchen.de.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
D
273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
E
209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
F
201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
G
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
H
177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
I
149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
N
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
O
123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
Q
136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
R
127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
S
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
T
115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
U
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
V
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
W
110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
X
100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
Y
104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
Z
94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
0
85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
2
63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
3
59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
4
70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
6
55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
7
46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
8
65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
Find proteins for P0A7W7 (Escherichia coli (strain K12))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
Find proteins for P0A7S9 (Escherichia coli (strain K12))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
102Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
GTP pyrophosphokinase,GTP pyrophosphokinase,GTP pyrophosphokinase
z
819Escherichia coliEscherichia coli O157:H7Mutation(s): 0 
Gene Names: relAZ4099ECs3644
EC: 2.7.6.5
Find proteins for P0AG20 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
P
144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
1
78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
5
57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
9
38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
240Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
Find proteins for P0A7R5 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
J
165Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
Find proteins for P0A7J3 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
K
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAA2903Escherichia coli K-12

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli K-12

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Entity ID: 32
MoleculeChainsLengthOrganism
16S ribosomal RNAa1539Escherichia coli K-12
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Entity ID: 51
MoleculeChainsLengthOrganism
mRNAv6Escherichia coli

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Entity ID: 52
MoleculeChainsLengthOrganism
P-site tRNAx77Escherichia coli K-12

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Entity ID: 58
MoleculeChainsLengthOrganism
deacylated A/R-tRNAy73Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721
German Research FoundationGermanyFOR-1805
SPPGermany1879
SFBGermany464
Swedish Research CouncilSweden2013-4680

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations, Experimental preparation
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 2.0: 2019-02-20
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 2.1: 2019-10-02
    Changes: Data collection, Other