3JAN

Structure of the scanning state of the mammalian SRP-ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.

Voorhees, R.M.Hegde, R.S.

(2015) Elife 4: --

  • DOI: 10.7554/eLife.07975
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, a ...

    The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL2
A
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL18
D
292N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL8
G
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL6
H
190N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL5
J
170N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL13
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL14
M
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL15
N
203N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL13
O
201N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL18
Q
187N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL19
R
180N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL20
S
175N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL21
T
159N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL22
U
99N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL14
V
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL23
X
119N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL24
Y
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL27
Z
135N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL15
a
147N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL29
b
75N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL30
c
94N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL31
d
107N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL32
e
128N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL33
f
109N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL34
g
114N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL29
h
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL36
i
102N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL38
k
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL39
l
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL40
m
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL42
o
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL3
B
394N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL4
C
367N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL6
E
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL30
F
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL16
I
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL22
P
153N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL24
W
63N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL37
j
86N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL41
n
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL43
p
91N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL28
r
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL11
K
163N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL10
q
202N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
SRP54
z
426N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
SRP19
9
105N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
SRP68
6
179N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS2
SA
208N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS1
SB
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS5
SC
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS4
SE
262N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS6
SG
237N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS7
SH
189N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS8
SI
206N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS4
SJ
185N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS17
SL
152N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS15
SN
149N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS11
SO
136N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS21
SV
82N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS8
SW
129N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS12
SX
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS24
SY
126N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS26
Sa
98N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS27
Sb
83N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS30
Se
57N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS3
SD
227N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS7
SF
191N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS10
SK
98N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS12
SM
124N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS19
SP
96N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS9
SQ
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS17
SR
129N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS13
SS
137N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS19
ST
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS10
SU
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein es25
SZ
75N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS28
Sc
64N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS14
Sd
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 85
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS31
Sf
71N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein RACK1
Sg
313N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 87
MoleculeChainsSequence LengthOrganismDetails
SRP9
S1
74N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 88
MoleculeChainsSequence LengthOrganismDetails
SRP14
S4
76N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsLengthOrganism
28S ribosomal RNA53658Oryctolagus cuniculus
Entity ID: 33
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus
Entity ID: 34
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8156Oryctolagus cuniculus
Entity ID: 49
MoleculeChainsLengthOrganism
Val tRNA376Oryctolagus cuniculus
Entity ID: 50
MoleculeChainsLengthOrganism
SRP 7S RNA4206Oryctolagus cuniculus
Entity ID: 53
MoleculeChainsLengthOrganism
18S ribosomal RNAS21742Oryctolagus cuniculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
5, 7, 8, D, g, S2, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
z
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-12-30
    Type: Database references