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Real space refined coordinates of the 30S subunit fitted into the low resolution cryo-EM map of the initiation-like state of E. coli 70S ribosome

by single particle reconstruction, at 11.5 A resolution

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Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1p87
TitleReal space refined coordinates of the 30S subunit fitted into the low resolution cryo-EM map of the initiation-like state of E. coli 70S ribosome
Descriptor30S Ribosomal Subunit
KeywordsRIBOSOME, EFG-GTP-bound state, ratchet-like movement, real-space refinement
AuthorsGao, H., Sengupta, J., Valle, M., Korostelev, A, Eswar, N., Stagg, S.M., Van Roey, P., Agrawal, R.K., Harvey, S.T., Sali, A., Chapman, M.S., Frank, J.
DateDeposition: 2003-05-06, Release: 2003-06-17
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
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PDB-1p86

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Article
Citation - primary
ArticleCell, Vol. 113, Issue 6, Page 789-801, Year 2003
TitleStudy of the structural dynamics of the E coli 70S ribosome using real-space refinement.
AuthorsHaixiao Gao, Jayati Sengupta, Mikel Valle, Andrei Korostelev, Narayanan Eswar, Scott M Stagg, Patrick Van Roey, Rajendra K Agrawal, Stephen C Harvey, Andrej Sali, Michael S Chapman, Joachim Frank
Howard Hughes Medical Institute, Health Research, Inc, Empire State Plaza, Albany, NY 12201, USA.
KeywordsBacterial Proteins (chemistry), Escherichia coli (genetics), Macromolecular Substances, Models, Molecular, Molecular Conformation, Molecular Weight, Protein Biosynthesis (physiology), Protein Structure, Quaternary (physiology), Protein Structure, Tertiary (physiology), RNA (chemistry, 63231-63-0), Ribosomal Proteins (chemistry), Ribosomes (chemistry)
LinksPubMed: 12809609, PII: S0092867403004276
Citation - 1
ArticleCell(Cambridge,Mass.), Vol. 100, Page: 537 - 549, Year: 2000,
TitleSolution structure of the E. coli 70S ribosome at 11.5 A resolution
AuthorsGabashvili, I.S., Agrawal, R.K., Spahn, C.M.T., Grassucci, R., Svergun, D.I., Frank, J., Penczek, P.
Citation - 2
ArticleNature, Vol. 406, Page: 318 - 322, Year: 2000,
TitleA ratchet-like inter-subunit reorganization of the ribosome during translocation
AuthorsFrank, J., Agrawal, R.K.
Components
ID 1 : 16S RIBOSOMAL RNA
Image
Description16S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight499996.344 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli


Strain: MRE 600
LinksGenBank: V00348, Sequence view
ID 2 : 30S RIBOSOMAL PROTEIN S2
Image
Description30S RIBOSOMAL PROTEIN S2
Typepolypeptide(L)
Formula weight26650.656 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02351, Sequence view
ID 3 : 30S RIBOSOMAL PROTEIN S3
Image
Description30S RIBOSOMAL PROTEIN S3
Typepolypeptide(L)
Formula weight25900.342 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02352, Sequence view
ID 4 : 30S RIBOSOMAL PROTEIN S4
Image
Description30S RIBOSOMAL PROTEIN S4
Typepolypeptide(L)
Formula weight23383.191 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02354, Sequence view
ID 5 : 30S RIBOSOMAL PROTEIN S5
Image
Description30S RIBOSOMAL PROTEIN S5
Typepolypeptide(L)
Formula weight17498.340 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02356, Sequence view
ID 6 : 30S RIBOSOMAL PROTEIN S6
Image
Description30S RIBOSOMAL PROTEIN S6
Typepolypeptide(L)
Formula weight15727.645 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02358, Sequence view
ID 7 : 30S RIBOSOMAL PROTEIN S7
Image
Description30S RIBOSOMAL PROTEIN S7
Typepolypeptide(L)
Formula weight19924.133 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02359, Sequence view
ID 8 : 30S RIBOSOMAL PROTEIN S8
Image
Description30S RIBOSOMAL PROTEIN S8
Typepolypeptide(L)
Formula weight14015.469 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02361, Sequence view
ID 9 : 30S RIBOSOMAL PROTEIN S9
Image
Description30S RIBOSOMAL PROTEIN S9
Typepolypeptide(L)
Formula weight14755.199 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02363, Sequence view
ID 10 : 30S RIBOSOMAL PROTEIN S10
Image
Description30S RIBOSOMAL PROTEIN S10
Typepolypeptide(L)
Formula weight11755.708 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02364, Sequence view
ID 11 : 30S RIBOSOMAL PROTEIN S11
Image
Description30S RIBOSOMAL PROTEIN S11
Typepolypeptide(L)
Formula weight13739.899 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02366, Sequence view
ID 12 : 30S RIBOSOMAL PROTEIN S12
Image
Description30S RIBOSOMAL PROTEIN S12
Typepolypeptide(L)
Formula weight13637.070 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02367, Sequence view
ID 13 : 30S RIBOSOMAL PROTEIN S13
Image
Description30S RIBOSOMAL PROTEIN S13
Typepolypeptide(L)
Formula weight12997.379 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02369, Sequence view
ID 14 : 30S RIBOSOMAL PROTEIN S14
Image
Description30S RIBOSOMAL PROTEIN S14
Typepolypeptide(L)
Formula weight11475.461 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02370, Sequence view
ID 15 : 30S RIBOSOMAL PROTEIN S15
Image
Description30S RIBOSOMAL PROTEIN S15
Typepolypeptide(L)
Formula weight10159.713 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02371, Sequence view
ID 16 : 30S RIBOSOMAL PROTEIN S16
Image
Description30S RIBOSOMAL PROTEIN S16
Typepolypeptide(L)
Formula weight9207.662 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02372, Sequence view
ID 17 : 30S RIBOSOMAL PROTEIN S17
Image
Description30S RIBOSOMAL PROTEIN S17
Typepolypeptide(L)
Formula weight9593.380 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02373, Sequence view
ID 18 : 30S RIBOSOMAL PROTEIN S18
Image
Description30S RIBOSOMAL PROTEIN S18
Typepolypeptide(L)
Formula weight8874.362 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02374, Sequence view
ID 19 : 30S RIBOSOMAL PROTEIN S19
Image
Description30S RIBOSOMAL PROTEIN S19
Typepolypeptide(L)
Formula weight10324.260 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02375, Sequence view
ID 20 : 30S RIBOSOMAL PROTEIN S20
Image
Description30S RIBOSOMAL PROTEIN S20
Typepolypeptide(L)
Formula weight9577.354 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
Strain: MRE 600
LinksUniProt: P02378, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameE. coli 70S ribosome bound with formyl-methionyl initiator tRNA
Buffer
Namehepes
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration32 mg/ml
Vitrification
DetailsRapid-freezing in liquid ethane
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F20
Date1997-07-01
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose1000 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 51200 X, Nominal: 51200 X
CsNominal: 2.0 mm
Nominal defocusMax: 4340 nm, Min: 730 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature93 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Software nameRSRef, TNT
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size2.93 A/pix
CTF correction methodCTF correction of 3D-maps
DetailsSPIDER package
Magnification calibrationTMV
MethodReference based alignment
Nominal pixel size2.93 A/pix
Resolution11.5 A
3D fitting
Methodauto
Refinement ProtocolMulti-rigid body, real-space refinement
Refinement SpaceREAL
Software nameRSRef, TNT
Target criteriacross-correlation coefficient, real space R factor
3D fitting list
3D Fitting ID1
PDB entry ID1IBL, 1FJG, 1FFK, 1JJ2, 1LNR, 1GIY
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms3622
Nucleic acid atoms1487
Protein atoms2135
Download
PDB format
Allpdb1p87.ent.gz
pdb1p87.ent (uncompressed file)
Header onlypdb1p87.ent.gz
mmCIF format
mmCIF1p87.cif.gz
XML format
All1p87.xml.gz
No-atom1p87-noatom.xml.gz
Ext-atom1p87-extatom.xml.gz
Movie files
movie #1
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.webm (WebM/VP8 format), 3.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.8 MB