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: https://doi.org/10.1126/science.aar7924
  • Primary Citation of Related Structures:  
    6FRK

  • 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 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.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL28C [auth 3]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L12D [auth 4]163Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0F [auth 6]202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L8I [auth A]244Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL3J [auth B]394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL4K [auth C]367Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL18L [auth D]292Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL6M [auth E]236Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL30N [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL8O [auth G]238Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL6P [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL16Q [auth I]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL5R [auth J]170Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL13S [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL14T [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15U [auth N]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL13V [auth O]201Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL22W [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL18X [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL19Y [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL20Z [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL21AA [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL22BA [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23CA [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL24DA [auth W]63Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL23EA [auth X]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL24FA [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GA [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL15HA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29IA [auth b]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL30JA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL31KA [auth d]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL32LA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL33MA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL34NA [auth g]114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL29OA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL36PA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37QA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL38RA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL39SA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL40TA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL41UA [auth n]23Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL42VA [auth o]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL43WA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP19XA [auth q]105Canis lupus familiarisMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72YA [auth r]605Canis lupus familiarisMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Signal sequenceZA [auth t]11Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68AB [auth u]568Canis lupus familiarisMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
SRP receptor beta subunitBB [auth v]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRB
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 9 kDa proteinCB [auth w]74Canis lupus familiarisMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa proteinDB [auth x]504Canis lupus familiarisMutation(s): 0 
EC: 3.6.5.4
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
SRP receptor alpha subunitEB [auth y]657Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRA
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 14 kDa proteinFB [auth z]110Canis lupus familiarisMutation(s): 0 
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Find proteins for P16255 (Canis lupus familiaris)
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Entity ID: 1
MoleculeChains LengthOrganismImage
Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNAA [auth 1]299Canis lupus familiaris
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Entity ID: 2
MoleculeChains LengthOrganismImage
tRNAB [auth 2]76Oryctolagus cuniculus
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Entity ID: 5
MoleculeChains LengthOrganismImage
28S ribosomal RNAE [auth 5]3,658Oryctolagus cuniculus
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Entity ID: 7
MoleculeChains LengthOrganismImage
5S ribosomal RNAG [auth 7]120Oryctolagus cuniculus
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Entity ID: 8
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAH [auth 8]156Oryctolagus cuniculus
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
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KG [auth v]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GNP
Query on GNP
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LG [auth x],
NG [auth y]		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN
Query on ZN
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GG [auth j],
HG [auth m],
IG [auth o]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AC [auth 5]
AD [auth 5]
AE [auth 5]
AF [auth 5]
AG [auth 8]
AC [auth 5],
AD [auth 5],
AE [auth 5],
AF [auth 5],
AG [auth 8],
BC [auth 5],
BD [auth 5],
BE [auth 5],
BF [auth 5],
BG [auth 8],
CC [auth 5],
CD [auth 5],
CE [auth 5],
CF [auth 5],
CG [auth 8],
DC [auth 5],
DD [auth 5],
DE [auth 5],
DF [auth 5],
DG [auth P],
EC [auth 5],
ED [auth 5],
EE [auth 5],
EF [auth 5],
EG [auth V],
FC [auth 5],
FD [auth 5],
FE [auth 5],
FF [auth 5],
FG [auth g],
GB [auth 5],
GC [auth 5],
GD [auth 5],
GE [auth 5],
GF [auth 5],
HB [auth 5],
HC [auth 5],
HD [auth 5],
HE [auth 5],
HF [auth 5],
IB [auth 5],
IC [auth 5],
ID [auth 5],
IE [auth 5],
IF [auth 5],
JB [auth 5],
JC [auth 5],
JD [auth 5],
JE [auth 5],
JF [auth 5],
JG [auth v],
KB [auth 5],
KC [auth 5],
KD [auth 5],
KE [auth 5],
KF [auth 5],
LB [auth 5],
LC [auth 5],
LD [auth 5],
LE [auth 5],
LF [auth 5],
MB [auth 5],
MC [auth 5],
MD [auth 5],
ME [auth 5],
MF [auth 5],
MG [auth x],
NB [auth 5],
NC [auth 5],
ND [auth 5],
NE [auth 5],
NF [auth 5],
OB [auth 5],
OC [auth 5],
OD [auth 5],
OE [auth 5],
OF [auth 5],
OG [auth y],
PB [auth 5],
PC [auth 5],
PD [auth 5],
PE [auth 5],
PF [auth 5],
QB [auth 5],
QC [auth 5],
QD [auth 5],
QE [auth 5],
QF [auth 5],
RB [auth 5],
RC [auth 5],
RD [auth 5],
RE [auth 5],
RF [auth 5],
SB [auth 5],
SC [auth 5],
SD [auth 5],
SE [auth 5],
SF [auth 5],
TB [auth 5],
TC [auth 5],
TD [auth 5],
TE [auth 5],
TF [auth 5],
UB [auth 5],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth 5],
VB [auth 5],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth 7],
WB [auth 5],
WC [auth 5],
WD [auth 5],
WE [auth 5],
WF [auth 7],
XB [auth 5],
XC [auth 5],
XD [auth 5],
XE [auth 5],
XF [auth 7],
YB [auth 5],
YC [auth 5],
YD [auth 5],
YE [auth 5],
YF [auth 7],
ZB [auth 5],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5],
ZF [auth 7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland51NF40_141735
Swiss National Science FoundationSwitzerland310030B_163478

Revision History  (Full details and data files)

  • 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