2J28

MODEL OF E. COLI SRP BOUND TO 70S RNCS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Following the Signal Sequence from Ribosomal Tunnel Exit to Signal Recognition Particle

Halic, M.Blau, M.Becker, T.Mielke, T.Pool, M.R.Wild, K.Sinning, I.Beckmann, R.

(2006) Nature 444: 508-511

  • DOI: https://doi.org/10.1038/nature05326
  • Primary Citation of Related Structures:  
    2J28, 2J37

  • PubMed Abstract: 

    Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.


  • Organizational Affiliation

    Gene Center, Department of Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32A [auth 0]56Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33B [auth 1]54Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34C [auth 2]46Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35D [auth 3]64Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36E [auth 4]38Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
SIGNAL SEQUENCEF [auth 7]18Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 54H [auth 9]430Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2K [auth C]267Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3L [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4M [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5N [auth F]178Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6O [auth G]176Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9P [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11Q [auth I]141Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13R [auth J]140Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14S [auth K]121Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15T [auth L]144Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16U [auth M]136Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17V [auth N]127Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18W [auth O]117Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19X [auth P]114Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20Y [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21Z [auth R]103Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22AA [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23BA [auth T]99Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24CA [auth U]102Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25DA [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27EA [auth W]84Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29FA [auth X]63Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30GA [auth Y]58Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31HA [auth Z]70Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains LengthOrganismImage
4.5S SIGNAL RECOGNITION PARTICLE RNAG [auth 8]74Escherichia coli
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAI [auth A]117Escherichia coli
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAJ [auth B]2,904Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth B]
AC [auth B]
AD [auth B]
AE [auth B]
BB [auth B]
AB [auth B],
AC [auth B],
AD [auth B],
AE [auth B],
BB [auth B],
BC [auth B],
BD [auth B],
BE [auth B],
CB [auth B],
CC [auth B],
CD [auth B],
CE [auth B],
DB [auth B],
DC [auth B],
DD [auth B],
DE [auth B],
EB [auth B],
EC [auth B],
ED [auth B],
EE [auth B],
FB [auth B],
FC [auth B],
FD [auth B],
FE [auth B],
GB [auth B],
GC [auth B],
GD [auth B],
GE [auth B],
HB [auth B],
HC [auth B],
HD [auth B],
HE [auth B],
IA [auth B],
IB [auth B],
IC [auth B],
ID [auth B],
IE [auth B],
JA [auth B],
JB [auth B],
JC [auth B],
JD [auth B],
JE [auth B],
KA [auth B],
KB [auth B],
KC [auth B],
KD [auth B],
KE [auth B],
LA [auth B],
LB [auth B],
LC [auth B],
LD [auth B],
LE [auth B],
MA [auth B],
MB [auth B],
MC [auth B],
MD [auth B],
ME [auth B],
NA [auth B],
NB [auth B],
NC [auth B],
ND [auth B],
NE [auth B],
OA [auth B],
OB [auth B],
OC [auth B],
OD [auth B],
OE [auth N],
PA [auth B],
PB [auth B],
PC [auth B],
PD [auth B],
QA [auth B],
QB [auth B],
QC [auth B],
QD [auth B],
RA [auth B],
RB [auth B],
RC [auth B],
RD [auth B],
SA [auth B],
SB [auth B],
SC [auth B],
SD [auth B],
TA [auth B],
TB [auth B],
TC [auth B],
TD [auth B],
UA [auth B],
UB [auth B],
UC [auth B],
UD [auth B],
VA [auth B],
VB [auth B],
VC [auth B],
VD [auth B],
WA [auth B],
WB [auth B],
WC [auth B],
WD [auth B],
XA [auth B],
XB [auth B],
XC [auth B],
XD [auth B],
YA [auth B],
YB [auth B],
YC [auth B],
YD [auth B],
ZA [auth B],
ZB [auth B],
ZC [auth B],
ZD [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-04-19
    Changes: Other
  • Version 1.4: 2017-08-30
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2018-10-03
    Changes: Data collection, Derived calculations