6FRK

Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting 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 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
  • Structures With Same Primary Citation

  • 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·SR 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. ban@mol.biol.ethz.ch.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL28
3
125Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L12
4
163Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
6
202Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L8
A
244Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL3
B
394Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL4
C
367Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL18
D
292Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL6
E
236Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL30
F
225Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL8
G
238Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL6
H
190Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL16
I
213Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL5
J
170Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL13
L
210Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL14
M
138Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
N
203Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL13
O
201Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL22
P
153Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL18
Q
187Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL19
R
180Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL20
S
175Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL21
T
159Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL22
U
99Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L23
V
131Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL24
W
63Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL23
X
119Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL24
Y
134Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
Z
135Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL15
a
147Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
75Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL30
c
94Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL31
d
107Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL32
e
128Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL33
f
109Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL34
g
114Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL29
h
122Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL36
i
102Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
j
86Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL38
k
69Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL39
l
50Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL40
m
52Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL41
n
23Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL42
o
104Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL43
p
91Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  J9PAS6

Find similar proteins by: Sequence  |  Structure

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 
Find proteins for P33731 (Canis lupus familiaris)
Go to UniProtKB:  P33731
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Signal sequence
t
11Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  Q00004

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  G1STG2

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  P21262

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  P61010

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  G1TCX6

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  P16255

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA1299Canis lupus familiaris

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
tRNA276Oryctolagus cuniculus

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 5
MoleculeChainsLengthOrganism
28S ribosomal RNA53658Oryctolagus cuniculus

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 7
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 8
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8156Oryctolagus cuniculus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

Download CCD File 
x, y
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
5, 7, 8, P, V, g, v, x, y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-02
    Changes: Data collection, Database references