6TC3

Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.7 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

Ornithine capture by a translating ribosome controls bacterial polyamine synthesis

Herrero del Valle, A.Seip, B.Cervera-Marzal, I.Sacheau, G.Seefeldt, A.C.Innis, C.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
S021
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
S031
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
S041
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: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
S051
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: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
S061
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
S071
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
S081
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
S091
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
S101
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: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
S111
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
S121
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: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
S131
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
S141
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
S151
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: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
S161
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
S171
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: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
S181
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S191
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
S201
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
S211
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
L021
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
L031
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
L041
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: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
L051
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
L061
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
L091
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
L311
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
L131
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L141
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L151
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
L161
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
L171
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
L181
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
L191
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
L201
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: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
L211
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
L221
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: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
L231
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
L241
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
L251
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
L271
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
L281
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
L291
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
L301
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
L321
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
L331
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
L341
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: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
L351
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
L361
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
SpeFL
SPE1
34Escherichia coli (strain K12)Mutation(s): 0 
Find proteins for A0A4S4NWS2 (Escherichia coli (strain K12))
Go to UniProtKB:  A0A4S4NWS2
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNA16S11534Escherichia coli K-12
Entity ID: 22
MoleculeChainsLengthOrganism
23S rRNA23S12897Escherichia coli K-12
Entity ID: 23
MoleculeChainsLengthOrganism
5S rRNA05S1120Escherichia coli K-12
Entity ID: 54
MoleculeChainsLengthOrganism
mRNAMRN17Escherichia coli K-12
Entity ID: 55
MoleculeChainsLengthOrganism
P-site Arg-tRNAPTR176Escherichia coli K-12
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
05S1, 16S1, 23S1, L031
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
L311, L361, S021
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
05S1, 16S1, 23S1, L021, L031, L041, L131, L141, L151, L161, L171, L181, L191, L201, L211, L221, L231, L241, L251, L271, L281, L321, L331, L341, L351, MRN1, PTR1, S021, S031, S081, S091, S111, S131, S171, SPE1
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
ORN
Query on ORN

Download SDF File 
Download CCD File 
23S1
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
16S1, 23S1, L231, PTR1, SPE1
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  21 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
16S1, 23S1, PTR1
RNA LINKINGC9 H13 N2 O9 PU
4D4
Query on 4D4
L161
L-peptide linkingC6 H14 N4 O3ARG
5MC
Query on 5MC
16S1, 23S1
RNA LINKINGC10 H16 N3 O8 PC
D2T
Query on D2T
S121
L-peptide linkingC5 H9 N O4 SASP
6MZ
Query on 6MZ
23S1
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
23S1
RNA LINKINGC10 H15 N2 O9 PU
RSP
Query on RSP
PTR1
RNA LINKINGC9 H14 N3 O7 P SC
1MG
Query on 1MG
23S1
RNA LINKINGC11 H16 N5 O8 PG
FME
Query on FME
SPE1
L-PEPTIDE LINKINGC6 H11 N O3 SMET
OMC
Query on OMC
23S1
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
16S1
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
PTR1
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
16S1, 23S1, PTR1
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
16S1, 23S1, PTR1
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
16S1
RNA LINKINGC10 H15 N2 O9 PU
MEQ
Query on MEQ
L031
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
OMG
Query on OMG
23S1
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
23S1, PTR1
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
23S1
RNA LINKINGC11 H16 N5 O7 PA
4OC
Query on 4OC
16S1
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
23S1
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council724040
European Molecular Biology Organization--
European UnioniNEXT grant 3901

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release