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
  • 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 ...

    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 LengthOrganismDetailsImage
Ribosomal protein eL28C [auth 3]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
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Ribosomal protein L12D [auth 4]163Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
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60S acidic ribosomal protein P0F [auth 6]202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
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Ribosomal protein L8I [auth A]244Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uL3J [auth B]394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uL4K [auth C]367Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
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Ribosomal protein uL18L [auth D]292Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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Ribosomal protein eL6M [auth E]236Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uL30N [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
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Ribosomal protein eL8O [auth G]238Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uL6P [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
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Ribosomal protein uL16Q [auth I]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
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Ribosomal protein uL5R [auth J]170Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
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Ribosomal protein eL13S [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
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Ribosomal protein eL14T [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
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Ribosomal protein L15U [auth N]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
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Ribosomal protein uL13V [auth O]201Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
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Ribosomal protein uL22W [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
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Ribosomal protein eL18X [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
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Ribosomal protein eL19Y [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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Ribosomal protein eL20Z [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
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Ribosomal protein eL21AA [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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Ribosomal protein eL22BA [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
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Ribosomal protein L23CA [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
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Ribosomal protein eL24DA [auth W]63Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
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Ribosomal protein uL23EA [auth X]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
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Ribosomal protein uL24FA [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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60S ribosomal protein L27GA [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
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Ribosomal protein uL15HA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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60S ribosomal protein L29IA [auth b]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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Ribosomal protein eL30JA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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Ribosomal protein eL31KA [auth d]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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Ribosomal protein eL32LA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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Ribosomal protein eL33MA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
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Ribosomal protein eL34NA [auth g]114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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Ribosomal protein uL29OA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
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Ribosomal protein eL36PA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
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Ribosomal protein L37QA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
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Ribosomal protein eL38RA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
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Ribosomal protein eL39SA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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Ribosomal protein eL40TA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
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Ribosomal protein eL41UA [auth n]23Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
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Ribosomal protein eL42VA [auth o]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
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Ribosomal protein eL43WA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP19XA [auth q]105Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72YA [auth r]605Canis lupus familiarisMutation(s): 0 
Gene Names: SRP72
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Find proteins for P33731 (Canis lupus familiaris)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Signal sequenceZA [auth t]11Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68AB [auth u]568Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
SRP receptor beta subunitBB [auth v]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRB
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Find proteins for G1STG2 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 9 kDa proteinCB [auth w]74Canis lupus familiarisMutation(s): 0 
Gene Names: SRP9
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa proteinDB [auth x]504Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
EC: 3.6.5
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
SRP receptor alpha subunitEB [auth y]657Oryctolagus cuniculusMutation(s): 0 
Gene Names: SRPRA
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 14 kDa proteinFB [auth z]110Canis lupus familiarisMutation(s): 0 
Gene Names: SRP14
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNAA [auth 1]299Canis lupus familiaris
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Entity ID: 2
MoleculeChainsLengthOrganismImage
tRNAB [auth 2]76Oryctolagus cuniculus
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Entity ID: 5
MoleculeChainsLengthOrganismImage
28S ribosomal RNAE [auth 5]3658Oryctolagus cuniculus
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Entity ID: 7
MoleculeChainsLengthOrganismImage
5S ribosomal RNAG [auth 7]120Oryctolagus cuniculus
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Entity ID: 8
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAH [auth 8]156Oryctolagus cuniculus
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

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KG [auth v]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GNP (Subject of Investigation/LOI)
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
 Ligand Interaction
ZN
Query on ZN

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GG [auth j], HG [auth m], IG [auth o]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AC [auth 5] , AD [auth 5] , AE [auth 5] , AF [auth 5] , AG [auth 8] , BC [auth 5] , BD [auth 5] , BE [auth 5] , 
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
 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  (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