7OBR

RNC-SRP early complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle.

Jomaa, A., Eitzinger, S., Zhu, Z., Chandrasekar, S., Kobayashi, K., Shan, S.O., Ban, N.

(2021) Cell Rep 36: 109350-109350

  • DOI: https://doi.org/10.1016/j.celrep.2021.109350
  • Primary Citation of Related Structures:  
    7OBQ, 7OBR

  • PubMed Abstract: 

    • Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles ...

    Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles. Due to its complexity, the mammalian SRP targeting process is mechanistically not well understood. In particular, it is not clear how SRP recognizes translating ribosomes with exposed signal sequences and how the GTPase activity of SRP and SR is regulated. Here, we present electron cryo-microscopy structures of SRP and SRP·SR in complex with the translating ribosome. The structures reveal the specific molecular interactions between SRP and the emerging signal sequence and the elements that regulate GTPase activity of SRP·SR. Our results suggest the molecular mechanism of how eukaryote-specific elements regulate the early and late stages of SRP-dependent protein targeting.

    Related Citations: 
    • Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle
      Jomaa, A., Eitzinger, S., Zhu, Z., Chandrasekar, S., Kobayashi, K., Shan, S., Ban, N.
      (2021) Cell Rep 36: --
    Organizational Affiliation: 

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth A]245Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 6
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uL3F [auth B]402Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
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60S ribosomal protein L4G [auth C]413Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
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60S ribosomal protein L5H [auth D]297Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6I [auth E]248Oryctolagus cuniculusMutation(s): 0 
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uL30J [auth F]225Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L7aK [auth G]319Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L9L [auth H]192Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L10M [auth I]214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Ribosomal protein L11N [auth J]178Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13O [auth L]210Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L14P [auth M]218Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Ribosomal protein L15Q [auth N]204Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13aR [auth O]199Oryctolagus cuniculusMutation(s): 0 
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uL22S [auth P]153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL17-C18orf32
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eL18T [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL19U [auth R]180Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L18aV [auth S]175Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL18A
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eL21W [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L22X [auth U]99Oryctolagus cuniculusMutation(s): 6 
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Ribosomal protein L23Y [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L24Z [auth W]63Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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uL23AA [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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Ribosomal protein L26BA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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60S ribosomal protein L27CA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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uL15DA [auth a]147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27A
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60S ribosomal protein L29EA [auth b]223Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L30FA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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eL31GA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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eL32HA [auth e]157Oryctolagus cuniculusMutation(s): 0 
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eL33IA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L34JA [auth g]129Oryctolagus cuniculusMutation(s): 0 
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uL29KA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36LA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37MA [auth j]97Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
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eL38NA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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eL39OA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL40PA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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60s ribosomal protein l41QA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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eL42RA [auth o]105Oryctolagus cuniculusMutation(s): 0 
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eL43SA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Signal recognition particle 19TA [auth q]144Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
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eL28UA [auth r]137Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL28
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Dipeptidyl aminopeptidase BVA [auth s]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DAP2, YHR028C
EC: 3.4.14
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 14 kDa proteinWA [auth t]110Canis lupus familiarisMutation(s): 0 
Gene Names: SRP14
UniProt
Find proteins for P16255 (Canis lupus familiaris)
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UniProt GroupP16255
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68XA [auth u]622Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
UniProt
Find proteins for Q00004 (Canis lupus familiaris)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 9 kDa proteinYA [auth w]86Canis lupus familiarisMutation(s): 0 
Gene Names: SRP9
UniProt
Find proteins for P21262 (Canis lupus familiaris)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa proteinZA [auth x]504Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
EC: 3.6.5
UniProt
Find proteins for P61010 (Canis lupus familiaris)
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP72AB [auth z]671Canis lupus familiarisMutation(s): 0 
Gene Names: SRP72
UniProt
Find proteins for P33731 (Canis lupus familiaris)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SRP RNAA [auth 1]249Canis lupus familiaris
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Entity ID: 2
MoleculeChainsLengthOrganismImage
28S rRNAB [auth 5]3,493Oryctolagus cuniculus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S ribosomal RNAC [auth 7]120Oryctolagus cuniculus
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Entity ID: 4
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAD [auth 8]156Oryctolagus cuniculus
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP
Download Ideal Coordinates CCD File 
ZE [auth x]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
UE [auth g],
VE [auth j],
WE [auth m],
XE [auth o],
YE [auth p]		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]
BB [auth 5]
BC [auth 5]
AC [auth 5],
AD [auth 5],
AE [auth 5],
BB [auth 5],
BC [auth 5],
BD [auth 5],
BE [auth 5],
CB [auth 5],
CC [auth 5],
CD [auth 5],
CE [auth 5],
DB [auth 5],
DC [auth 5],
DD [auth 5],
DE [auth 5],
EB [auth 5],
EC [auth 5],
ED [auth 5],
EE [auth 5],
FB [auth 5],
FC [auth 5],
FD [auth 5],
FE [auth 5],
GB [auth 5],
GC [auth 5],
GD [auth 5],
GE [auth 5],
HB [auth 5],
HC [auth 5],
HD [auth 5],
HE [auth 5],
IB [auth 5],
IC [auth 5],
ID [auth 5],
IE [auth 5],
JB [auth 5],
JC [auth 5],
JD [auth 5],
JE [auth 5],
KB [auth 5],
KC [auth 5],
KD [auth 5],
KE [auth 5],
LB [auth 5],
LC [auth 5],
LD [auth 5],
LE [auth 5],
MB [auth 5],
MC [auth 5],
MD [auth 5],
ME [auth 5],
NB [auth 5],
NC [auth 5],
ND [auth 5],
NE [auth 5],
OB [auth 5],
OC [auth 5],
OD [auth 5],
OE [auth 5],
PB [auth 5],
PC [auth 5],
PD [auth 5],
PE [auth 5],
QB [auth 5],
QC [auth 5],
QD [auth 5],
QE [auth 5],
RB [auth 5],
RC [auth 5],
RD [auth 5],
RE [auth 5],
SB [auth 5],
SC [auth 5],
SD [auth 5],
SE [auth 5],
TB [auth 5],
TC [auth 5],
TD [auth 5],
TE [auth 5],
UB [auth 5],
UC [auth 5],
UD [auth 5],
VB [auth 5],
VC [auth 5],
VD [auth 5],
WB [auth 5],
WC [auth 5],
WD [auth 5],
XB [auth 5],
XC [auth 5],
XD [auth 5],
YB [auth 5],
YC [auth 5],
YD [auth 5],
ZB [auth 5],
ZC [auth 5],
ZD [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references