6FRK

Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a prehandover mammalian ribosomal SRP·SRP receptor targeting complex.

Kobayashi, K.Jomaa, A.Lee, J.H.Chandrasekar, S.Boehringer, D.Shan, S.O.Ban, N.

(2018) Science 360: 323-327

  • DOI: 10.1126/science.aar7924

  • PubMed Abstract: 
  • Signal recognition particle (SRP) targets proteins to the endoplasmic reticulum (ER). SRP recognizes the ribosome synthesizing a signal sequence and delivers it to the SRP receptor (SR) on the ER membrane followed by the transfer of the signal sequen ...

    Signal recognition particle (SRP) targets proteins to the endoplasmic reticulum (ER). SRP recognizes the ribosome synthesizing a signal sequence and delivers it to the SRP receptor (SR) on the ER membrane followed by the transfer of the signal sequence to the translocon. Here, we present the cryo-electron microscopy structure of the mammalian translating ribosome in complex with SRP and SR in a conformation preceding signal sequence handover. The structure visualizes all eukaryotic-specific SRP and SR proteins and reveals their roles in stabilizing this conformation by forming a large protein assembly at the distal site of SRP RNA. We provide biochemical evidence that the guanosine triphosphate hydrolysis of SRP┬ĚSR is delayed at this stage, possibly to provide a time window for signal sequence handover to the translocon.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, Zurich CH-8093, Switzerland.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, Zurich CH-8093, Switzerland. ban@mol.biol.ethz.ch.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL28
3
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L12
4
163N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
6
202N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L8
A
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL3
B
394N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL4
C
367N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL18
D
292N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL6
E
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL30
F
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL8
G
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL6
H
190N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL16
I
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL5
J
170N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL13
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL14
M
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
N
203N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL13
O
201N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL22
P
153N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL18
Q
187N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL19
R
180N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL20
S
175N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL21
T
159N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL22
U
99N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L23
V
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL24
W
63N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL23
X
119N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL24
Y
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
Z
135N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL15
a
147N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
75N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL30
c
94N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL31
d
107N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL32
e
128N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL33
f
109N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL34
g
114N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL29
h
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL36
i
102N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
j
86N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL38
k
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL39
l
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL40
m
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL41
n
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL42
o
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL43
p
91N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP19
q
105Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
Find proteins for J9PAS6 (Canis lupus familiaris)
Go to Gene View: SRP19
Go to UniProtKB:  J9PAS6
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72
r
605Canis lupus familiarisMutation(s): 0 
Gene Names: SRP72
Find proteins for P33731 (Canis lupus familiaris)
Go to Gene View: SRP72
Go to UniProtKB:  P33731
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Signal sequence
t
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP68
u
568Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
Find proteins for Q00004 (Canis lupus familiaris)
Go to Gene View: SRP68
Go to UniProtKB:  Q00004
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
SRP receptor beta subunit
v
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRB
Find proteins for G1STG2 (Oryctolagus cuniculus)
Go to Gene View: SRPRB
Go to UniProtKB:  G1STG2
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 9 kDa protein
w
74Canis lupus familiarisMutation(s): 0 
Gene Names: SRP9
Find proteins for P21262 (Canis lupus familiaris)
Go to Gene View: SRP9
Go to UniProtKB:  P21262
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 54 kDa protein
x
504Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
Find proteins for P61010 (Canis lupus familiaris)
Go to Gene View: SRP54
Go to UniProtKB:  P61010
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
SRP receptor alpha subunit
y
657Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRA
Find proteins for G1TCX6 (Oryctolagus cuniculus)
Go to Gene View: SRPRA
Go to UniProtKB:  G1TCX6
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 14 kDa protein
z
110Canis lupus familiarisMutation(s): 0 
Gene Names: SRP14
Find proteins for P16255 (Canis lupus familiaris)
Go to Gene View: SRP14
Go to UniProtKB:  P16255
Entity ID: 1
MoleculeChainsLengthOrganism
Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA1299Canis lupus familiaris
Entity ID: 2
MoleculeChainsLengthOrganism
tRNA276Oryctolagus cuniculus
Entity ID: 5
MoleculeChainsLengthOrganism
28S ribosomal RNA53658Oryctolagus cuniculus
Entity ID: 7
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus
Entity ID: 8
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8156Oryctolagus cuniculus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
j, m, o
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
v
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
5, 7, 8, g, P, v, V, x, y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
x, y
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
r
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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
Swiss National Science FoundationSwitzerland51NF40_141735
Swiss National Science FoundationSwitzerland310030B_163478

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references