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. 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth A]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL3F [auth B]402Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4G [auth C]413Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5H [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth E]248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL30J [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aK [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9L [auth H]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10M [auth I]214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11N [auth J]178Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13O [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14P [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth N]204Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aR [auth O]199Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL22S [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL18T [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TX70 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL19U [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aV [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTY7 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL21W [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22X [auth U]99Oryctolagus cuniculusMutation(s): 6 
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Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23Y [auth V]140Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth W]63Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uL23AA [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26BA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27CA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uL15DA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth b]223Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30FA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL31GA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL32HA [auth e]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL33IA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34JA [auth g]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
uL29KA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36LA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37MA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL38NA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL39OA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL40PA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41QA [auth n]25Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL42RA [auth o]105Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D391 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eL43SA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 19TA [auth q]144Canis lupus familiarisMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eL28UA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl aminopeptidase BVA [auth s]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DAP2YHR028C
EC: 3.4.14
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 14 kDa proteinWA [auth t]110Canis lupus familiarisMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68XA [auth u]622Canis lupus familiarisMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 9 kDa proteinYA [auth w]86Canis lupus familiarisMutation(s): 0 
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UniProt GroupP21262
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa proteinZA [auth x]504Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P61010 (Canis lupus familiaris)
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UniProt GroupP61010
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP72AB [auth z]671Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P33731 (Canis lupus familiaris)
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UniProt GroupP33731
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Entity ID: 1
MoleculeChains LengthOrganismImage
SRP RNAA [auth 1]249Canis lupus familiaris
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S rRNAB [auth 5]3,493Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 7]120Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAD [auth 8]156Oryctolagus cuniculus
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Small Molecules
Ligands 3 Unique
IDChains Name / 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
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
MG
Query on MG

Download Ideal Coordinates CCD File 
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
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