5NCO

Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome.

Jomaa, A.Fu, Y.H.Boehringer, D.Leibundgut, M.Shan, S.O.Ban, N.

(2017) Nat Commun 8: 15470-15470

  • DOI: 10.1038/ncomms15470

  • PubMed Abstract: 
  • During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the t ...

    During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the translocon. Using electron cryo-microscopy, we have determined the structure of a quaternary complex of the translating Escherichia coli ribosome, the SRP-SR in the 'activated' state and the translocon. Our structure, supported by biochemical experiments, reveals that the SRP RNA adopts a kinked and untwisted conformation to allow repositioning of the 'activated' SRP-SR complex on the ribosome. In addition, we observe the translocon positioned through interactions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon. Our study provides new insights into the mechanism of signal sequence transfer from the SRP to the translocon.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH, Zurich CH-8093, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
271Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
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: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
I
125Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
J
134Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
125Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
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: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
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: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
95Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
76Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
62Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
a
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
51Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 32
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: 33
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: 34
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: 35
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecY
g
416Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secY (prlA)
Find proteins for P0AGA2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGA2
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecE
h
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secE (prlG)
Find proteins for P0AG96 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG96
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein
i
450Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ffh
Find proteins for P0AGD7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGD7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Protein-export membrane protein SecG
j
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secG
Find proteins for P0AG99 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG99
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Signal sequence (1A9L)
k
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle receptor FtsY
l
271Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ftsY
Find proteins for P10121 (Escherichia coli (strain K12))
Go to UniProtKB:  P10121
Entity ID: 1
MoleculeChainsLengthOrganism
4.5S SRP RNA (Ffs)1104Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
P-site tRNA-CCA end23Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
23S rRNAA2903Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
5S rRNAB120Escherichia coli
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
i, l
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
i, l
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
i, l
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
i
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 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
Swiss National Science FoundationSwitzerland--
National Consortium for RNA and DiseaseSwitzerland--

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2017-08-30
    Type: Data collection
  • Version 1.4: 2018-03-28
    Type: Structure summary