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Structure of the 50S subunit of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143

by single particle reconstruction, at 15 A resolution

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#1: Depositted structure unit, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1143, Made by Jmol

#3: With PDB-2gyb, Made by Jmol

#4: With PDB-2akh, PDB-2aki, PDB-2gyb, Made by Jmol

#5: Superimposing with EM 3D map: EMDB-1143 (with PDB-2akh, PDB-2aki, PDB-2gyb), Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2gyc
TitleStructure of the 50S subunit of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143
Descriptor50S RIBOSOMAL SUBUNIT
KeywordsRIBOSOME, SecM, nascent chain, signal transduction, RNA world, polypeptide exit tunnel, translocation, ribosome, elongation arrest, protein-conducting channel
AuthorsMitra, K., Frank, J.
DateDeposition: 2006-05-09, Release: 2006-09-26
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1143, Made by Jmol

#3: With PDB-2gyb, Made by Jmol

#4: With PDB-2akh, PDB-2aki, PDB-2gyb, Made by Jmol

#5: Superimposing with EM 3D map: EMDB-1143 (with PDB-2akh, PDB-2aki, PDB-2gyb), Made by UCSF CHIMERA

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PDB-2gyb

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Cite: data citing same article

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Article
Citation - primary
ArticleMol. Cell, Vol. 22, Issue 4, Page 533-43, Year 2006
TitleElongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
AuthorsKakoli Mitra, Christiane Schaffitzel, Felcy Fabiola, Michael S Chapman, Nenad Ban, Joachim Frank
Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, Empire State Plaza, Albany, New York 12201, USA.
KeywordsCryoelectron Microscopy, Escherichia coli (genetics), Escherichia coli Proteins (chemistry), Macromolecular Substances, Models, Molecular, Nucleic Acid Conformation, Peptide Chain Elongation, Translational, Protein Conformation, RNA, Bacterial (chemistry), RNA, Ribosomal (chemistry), RNA, Ribosomal, 23S (chemistry), Ribosomes (metabolism), SecM protein, E coli, Transcription Factors (chemistry)
LinksPII: S1097-2765(06)00294-2, DOI: 10.1016/j.molcel.2006.05.003, PubMed: 16713583
Citation - 1
ArticleNature, Vol. 438, Page: 318 - 324, Year: 2005,
TitleStructure of the E. coli protein-conducting channel bound to a translating ribosome
AuthorsMitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks III, C.L., Ban, N., Frank, J.
Citation - 2
ArticleCell(Cambridge,Mass.), Vol. 114, Page: 123 - 134, Year: 2003,
TitleLocking and unlocking of ribosomal motions
AuthorsValle, M., Zavialov, A.V., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J.
Citation - 3
ArticleFEBS Lett., Vol. 580, Issue 14, Page 3353-60, Year 2006
TitleA model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel.
AuthorsKakoli Mitra, Joachim Frank
Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsModels, Molecular, Protein Biosynthesis, Protein Conformation, Protein Transport, Ribosomes (metabolism)
LinksPII: S0014-5793(06)00609-0, DOI: 10.1016/j.febslet.2006.05.019, PubMed: 16714018
Components
ID 1 : 23S ribosomal RNA
Image
Description23S ribosomal RNA
Typepolyribonucleotide
Formula weight888504.688 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksSequence view
ID 2 : 5S ribosomal RNA
Image
Description5S ribosomal RNA
Typepolyribonucleotide
Formula weight34917.012 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 3 : 50S ribosomal protein L1
Image
Description50S ribosomal protein L1
Typepolypeptide(L)
Formula weight23591.438 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L0, Sequence view
ID 4 : 50S ribosomal protein L7/L12
Image
Description50S ribosomal protein L7/L12
Typepolypeptide(L)
Formula weight12090.999 Da
Number of molecules2
ID4
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K2, Sequence view
ID 5 : 50S ribosomal protein L2
Image
Description50S ribosomal protein L2
Typepolypeptide(L)
Formula weight24691.438 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60422, Sequence view
ID 6 : 50S ribosomal protein L3
Image
Description50S ribosomal protein L3
Typepolypeptide(L)
Formula weight22277.709 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60438, Sequence view
ID 7 : 50S ribosomal protein L4
Image
Description50S ribosomal protein L4
Typepolypeptide(L)
Formula weight21806.293 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60723, Sequence view
ID 8 : 50S ribosomal protein L5
Image
Description50S ribosomal protein L5
Typepolypeptide(L)
Formula weight20131.486 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P62399, Sequence view
ID 9 : 50S ribosomal protein L6
Image
Description50S ribosomal protein L6
Typepolypeptide(L)
Formula weight17799.543 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG55, Sequence view
ID 10 : 50S ribosomal protein L9
Image
Description50S ribosomal protein L9
Typepolypeptide(L)
Formula weight15789.174 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R1, Sequence view
ID 11 : 50S ribosomal protein L11
Image
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14577.119 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7J7, Sequence view
ID 12 : 50S ribosomal protein L13
Image
Description50S ribosomal protein L13
Typepolypeptide(L)
Formula weight16050.749 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AA10, Sequence view
ID 13 : 50S ribosomal protein L14
Image
Description50S ribosomal protein L14
Typepolypeptide(L)
Formula weight13433.980 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY3, Sequence view
ID 14 : 50S ribosomal protein L15
Image
Description50S ribosomal protein L15
Typepolypeptide(L)
Formula weight14477.937 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02413, Sequence view
ID 15 : 50S ribosomal protein L16
Image
Description50S ribosomal protein L16
Typepolypeptide(L)
Formula weight14736.614 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY7, Sequence view
ID 16 : 50S ribosomal protein L17
Image
Description50S ribosomal protein L17
Typepolypeptide(L)
Formula weight12945.183 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG44, Sequence view
ID 17 : 50S ribosomal protein L18
Image
Description50S ribosomal protein L18
Typepolypeptide(L)
Formula weight12273.206 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0C018, Sequence view
ID 18 : 50S ribosomal protein L19
Image
Description50S ribosomal protein L19
Typepolypeptide(L)
Formula weight13028.207 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K6, Sequence view
ID 19 : 50S ribosomal protein L20
Image
Description50S ribosomal protein L20
Typepolypeptide(L)
Formula weight13254.805 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L3, Sequence view
ID 20 : 50S ribosomal protein L22
Image
Description50S ribosomal protein L22
Typepolypeptide(L)
Formula weight11778.894 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P61175, Sequence view
ID 21 : 50S ribosomal protein L23
Image
Description50S ribosomal protein L23
Typepolypeptide(L)
Formula weight10205.105 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADZ0, Sequence view
ID 22 : 50S ribosomal protein L24
Image
Description50S ribosomal protein L24
Typepolypeptide(L)
Formula weight10823.674 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60624, Sequence view
ID 23 : 50S ribosomal protein L25
Image
Description50S ribosomal protein L25
Typepolypeptide(L)
Formula weight10713.566 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68919, Sequence view
ID 24 : 50S ribosomal protein L27
Image
Description50S ribosomal protein L27
Typepolypeptide(L)
Formula weight9015.426 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L8, Sequence view
ID 25 : 50S ribosomal protein L29
Image
Description50S ribosomal protein L29
Typepolypeptide(L)
Formula weight7087.321 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M6, Sequence view
ID 26 : 50S ribosomal protein L30
Image
Description50S ribosomal protein L30
Typepolypeptide(L)
Formula weight6223.421 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG51, Sequence view
ID 27 : 50S ribosomal protein L32
Image
Description50S ribosomal protein L32
Typepolypeptide(L)
Formula weight3317.813 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N4, Sequence view
ID 28 : 50S ribosomal protein L33
Image
Description50S ribosomal protein L33
Typepolypeptide(L)
Formula weight6015.169 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N9, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005878
Name30S ribosomal protein L1
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:008932
Name30S ribosomal protein L7/L12
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005880
Name30S ribosomal protein L2
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000597
Name30S ribosomal protein L3
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:013005
Name30S ribosomal protein L4
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:002132
Name30S ribosomal protein L5
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000702
Name30S ribosomal protein L6
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000244
Name30S ribosomal protein L9
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:006519
Name30S ribosomal protein L11
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005823
Name30S ribosomal protein L13
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005745
Name30S ribosomal protein L14
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005749
Name30S ribosomal protein L15
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000114
Name30S ribosomal protein L16
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000456
Name30S ribosomal protein L17
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:004389
Name30S ribosomal protein L18
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001857
Name30S ribosomal protein L19
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005812
Name30S ribosomal protein L20
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005727
Name30S ribosomal protein L22
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001014
Name30S ribosomal protein L23
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:003256
Name30S ribosomal protein L24
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001021
Name30S ribosomal protein L25
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001684
Name30S ribosomal protein L27
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001854
Name30S ribosomal protein L29
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005996
Name30S ribosomal protein L30
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:002677
Name30S ribosomal protein L32
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001705
Name30S ribosomal protein L33
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration32 mg/ml
Sample support
DetailsQuantifoil holey-Carbon film grids
Vitrification
Detailsrapid-freezing in liquid ethane
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Date2004-03-09
Electron gun
Electron sourcefield emission gun
Accelerating voltage300 kV
Electron dose1100 e/A**2
Illumination modeflood beam
Lens
Modebright field
MagnificationCalibrated: 39000 X, Nominal: 39000 X
CsNominal: 2.0 mm
Nominal defocusMax: 4.3 nm, Min: 1.5 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature93 Kelvin
Detector
TypeKODAK SO163 film
Processing
2D projection selection
Software nameCNS implementation of RSRef
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size3.59 A/pix
CTF correction methodCTF correction of 3D-maps by Wiener filtration
DetailsWITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RESOLUTION OF THE EM MAP. THE RESOLUTION OF THE ATOMIC MODEL FITTED INTO EMD-1143 (11.0 ANGSTROMS AT FSC 3SIGMA, 15.0 ANGSTROMS AT FSC 0.5) IS THUS ESTIMATED TO BE BETWEEN 2-3 ANGSTROMS. REAL-SPACE REFINEMENT USING RIGID BODIES INTO EM MAP EMD-1143. RIGID BODY DEFINITION: AN AUTONOMOUS SECONDARY STRUCTURE UNIT (E.G. HELIX SEGMENT, HAIRPIN) OF THE RIBOSOMAL RNA; AN AUTONOMOUS RIBOSOMAL PROTEIN DOMAIN. THE ATOMIC MODEL USED WAS GENERATED FROM E. COLI MODELS OF X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS. IN THE ABSENCE OF E. COLI MODELS, STRUCTURES WERE DERIVED DIRECTLY FROM THE X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS. RESOLUTION for FSC 3SIGMA (ANGSTROMS) is 11.000, RESOLUTION for FSC 0.5 (ANGSTROMS) is 15.000.
Magnification calibrationTMV
Method3D projection matching; conjugate gradients with regularization
Nominal pixel size3.59 A/pix
Resolution15 A
3D fitting
Refinement ProtocolCNS implementation of RSRef
Refinement SpaceREAL
Software nameCNS implementation of RSRef, spider
Target criteriaMinimization of number of poor van der Waals contacts and maximation of correlation coefficient
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms87129
Nucleic acid atoms61134
Protein atoms25995
Download
PDB format
Allpdb2gyc.ent.gz
pdb2gyc.ent (uncompressed file)
Header onlypdb2gyc.ent.gz
mmCIF format
mmCIF2gyc.cif.gz
XML format
All2gyc.xml.gz
No-atom2gyc-noatom.xml.gz
Ext-atom2gyc-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.9 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.5 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.1 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB