1EG0

FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 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

Solution structure of the E. coli 70S ribosome at 11.5 A resolution.

Gabashvili, I.S.Agrawal, R.K.Spahn, C.M.Grassucci, R.A.Svergun, D.I.Frank, J.Penczek, P.

(2000) Cell 100: 537-549


  • PubMed Abstract: 
  • Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and inters ...

    Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase-associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits.


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    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc., Albany, New York 11201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S4 RIBOSOMAL PROTEIN)
A
159Geobacillus stearothermophilusGene Names: rpsD
Find proteins for P81288 (Geobacillus stearothermophilus)
Go to UniProtKB:  P81288
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S5 RIBOSOMAL PROTEIN)
B
148Geobacillus stearothermophilusGene Names: rpsE
Find proteins for P02357 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02357
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S6 RIBOSOMAL PROTEIN)
C
97Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S7 RIBOSOMAL PROTEIN)
D
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S8 RIBOSOMAL PROTEIN)
E
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S15 RIBOSOMAL PROTEIN)
F
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S17 RIBOSOMAL PROTEIN)
G
93Geobacillus stearothermophilusGene Names: rpsQ
Find proteins for P23828 (Geobacillus stearothermophilus)
Go to UniProtKB:  P23828
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (S20 RIBOSOMAL PROTEIN)
H
100N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBOSOMAL PROTEIN L1)
N
229Thermus thermophilusGene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus)
Go to UniProtKB:  P27150
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBOSOMAL PROTEIN L6)
J
171Geobacillus stearothermophilusGene Names: rplF
Find proteins for P02391 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02391
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBOSOMAL PROTEIN L11)
K
140Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: rplK
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
Entity ID: 1
MoleculeChainsLengthOrganism
FRAGMENT OF 16S RRNA HELIX 23I33Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
FRAGMENT OF 23S RRNAL57Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
HELIX 95 OF 23S RRNAM26Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
FORMYL-METHIONYL-TRNAO76Escherichia coli
Small Molecules
Modified Residues  7 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
O
RNA LINKINGC9 H13 N2 O9 PU
OMC
Query on OMC
O
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
O
RNA LINKINGC9 H13 N2 O8 P SU
UNK
Query on UNK
H
L-PEPTIDE LINKINGC4 H9 N O2

--

N
Query on N
I
RNA LINKINGC5 H11 O7 P

--

5MU
Query on 5MU
O
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
O
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
SPIDERmodel building
Omodel building
SPIDERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance