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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL283125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L124163Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P06202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L8A244Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL3B394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL4C367Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL18D292Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL6E236Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL8G238Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL6H190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL16I213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL5J170Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL13L210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL14M138Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15N203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL13O201Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL22P153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL18Q187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL19R180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL20S175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL21T159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL22U99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L23V131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL24W63Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL24Y134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27Z135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL15a147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29b75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL30c94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL31d107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL33f109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL34g114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL29h122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37j86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL38k69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL39l50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL40m52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL42o104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL43p91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP19q105Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
Find proteins for J9PAS6 (Canis lupus familiaris)
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Go to UniProtKB:  J9PAS6
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72r605Canis lupus familiarisMutation(s): 0 
Gene Names: SRP72
Find proteins for P33731 (Canis lupus familiaris)
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Go to UniProtKB:  P33731
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Signal sequencet11Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP68u568Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
Find proteins for Q00004 (Canis lupus familiaris)
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Go to UniProtKB:  Q00004
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 9 kDa proteinw74Canis lupus familiarisMutation(s): 0 
Gene Names: SRP9
Find proteins for P21262 (Canis lupus familiaris)
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Go to UniProtKB:  P21262
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
SRP receptor alpha subunity657Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRA
Find proteins for G1TCX6 (Oryctolagus cuniculus)
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Go to UniProtKB:  G1TCX6
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 14 kDa proteinz110Canis lupus familiarisMutation(s): 0 
Gene Names: SRP14
Find proteins for P16255 (Canis lupus familiaris)
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Go to UniProtKB:  P16255
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL30F225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL23X119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL32e128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL36i102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL41n23Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
SRP receptor beta subunitv213Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRB
Find proteins for G1STG2 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 54 kDa proteinx504Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
Find proteins for P61010 (Canis lupus familiaris)
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Go to UniProtKB:  P61010
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Entity ID: 5
MoleculeChainsLengthOrganism
28S ribosomal RNA53658Oryctolagus cuniculus

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Entity ID: 7
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus

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Entity ID: 8
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8156Oryctolagus cuniculus

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

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Entity ID: 2
MoleculeChainsLengthOrganism
tRNA276Oryctolagus cuniculus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

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

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

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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

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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