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MODEL OF E. COLI SRP BOUND TO 70S RNCS

by single particle reconstruction, at 8 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1261, Image by UCSF CHIMERA

#3: Superimposing with EM 3D map: EMDB-1262, Image by UCSF CHIMERA

#4: Superimposing with EM 3D map: EMDB-1263, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2j28
TitleMODEL OF E. COLI SRP BOUND TO 70S RNCS
DescriptorSIGNAL SEQUENCE
SIGNAL RECOGNITION PARTICLE 54
(50S ribosomal protein ...) x 28
KeywordsRIBOSOME, PROTEIN-RNA COMPLEX, SIGNAL RECOGNITION PARTICLE
AuthorsHalic, M., Blau, M., Becker, T., Mielke, T., Pool, M.R., Wild, K., Sinning, I., Beckmann, R.
DateDeposition: 2006-08-16, Release: 2006-11-08
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1261, Image by UCSF CHIMERA

#3: Superimposing with EM 3D map: EMDB-1262, Image by UCSF CHIMERA

#4: Superimposing with EM 3D map: EMDB-1263, Image by UCSF CHIMERA

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EMDB-1261

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EMDB-1262

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EMDB-1263

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Article
Citation - primary
ArticleNature, Vol. 444, Issue 7118, Page 507-11, Year 2006
TitleFollowing the signal sequence from ribosomal tunnel exit to signal recognition particle.
AuthorsMario Halic, Michael Blau, Thomas Becker, Thorsten Mielke, Martin R Pool, Klemens Wild, Irmgard Sinning, Roland Beckmann
Gene Center, Department of Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
KeywordsAnimals, Base Sequence, Escherichia coli (genetics), Mammals (genetics), Models, Molecular, Molecular Sequence Data, Protein Biosynthesis, Protein Sorting Signals, RNA, Ribosomal (chemistry), Ribosomes (chemistry), Signal Recognition Particle (chemistry)
LinksDOI: 10.1038/nature05326, PubMed: 17086193
Components
ID 1 : 50S RIBOSOMAL PROTEIN L32
Image
Description50S RIBOSOMAL PROTEIN L32
Typepolypeptide(L)
Formula weight6332.307 Da
Number of molecules1
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI

LinksUniProt: P0A7N4, Sequence view
ID 2 : 50S RIBOSOMAL PROTEIN L33
Image
Description50S RIBOSOMAL PROTEIN L33
Typepolypeptide(L)
Formula weight6257.510 Da
Number of molecules1
ID2
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7N9, Sequence view
ID 3 : 50S RIBOSOMAL PROTEIN L34
Image
Description50S RIBOSOMAL PROTEIN L34
Typepolypeptide(L)
Formula weight5397.506 Da
Number of molecules1
ID3
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7P5, Sequence view
ID 4 : 50S RIBOSOMAL PROTEIN L35
Image
Description50S RIBOSOMAL PROTEIN L35
Typepolypeptide(L)
Formula weight7181.907 Da
Number of molecules1
ID4
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7Q2, Sequence view
ID 5 : 50S RIBOSOMAL PROTEIN L36
Image
Description50S RIBOSOMAL PROTEIN L36
Typepolypeptide(L)
Formula weight4377.415 Da
Number of molecules1
ID5
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7Q6, Sequence view
ID 6 : SIGNAL SEQUENCE
Image
DescriptionSIGNAL SEQUENCE
Typepolypeptide(L)
Formula weight2121.567 Da
Number of molecules1
ID6
SourceMethod: Obtained synthetically
LinksSequence view
ID 7 : 4.5S SIGNAL RECOGNITION PARTICLE RNA
Image
Description4.5S SIGNAL RECOGNITION PARTICLE RNA
Typepolyribonucleotide
Formula weight23968.469 Da
Number of molecules1
ID7
SourceMethod: Obtained synthetically
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksSequence view
ID 8 : SIGNAL RECOGNITION PARTICLE 54
Image
DescriptionSIGNAL RECOGNITION PARTICLE 54
Typepolypeptide(L)
Formula weight47362.551 Da
Number of molecules1
ID8
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0AGD7, Sequence view
ID 9 : 5S RIBOSOMAL RNA
Image
Description5S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight37848.766 Da
Number of molecules1
ID9
SourceMethod: Obtained synthetically
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksSequence view
ID 10 : 23S RIBOSOMAL RNA
Image
Description23S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight941613.688 Da
Number of molecules1
ID10
SourceMethod: Obtained synthetically
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksSequence view
ID 11 : 50S RIBOSOMAL PROTEIN L2
Image
Description50S RIBOSOMAL PROTEIN L2
Typepolypeptide(L)
Formula weight29248.984 Da
Number of molecules1
ID11
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P60422, Sequence view
ID 12 : 50S RIBOSOMAL PROTEIN L3
Image
Description50S RIBOSOMAL PROTEIN L3
Typepolypeptide(L)
Formula weight22277.709 Da
Number of molecules1
ID12
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P60438, Sequence view
ID 13 : 50S RIBOSOMAL PROTEIN L4
Image
Description50S RIBOSOMAL PROTEIN L4
Typepolypeptide(L)
Formula weight22121.723 Da
Number of molecules1
ID13
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P60723, Sequence view
ID 14 : 50S RIBOSOMAL PROTEIN L5
Image
Description50S RIBOSOMAL PROTEIN L5
Typepolypeptide(L)
Formula weight20202.566 Da
Number of molecules1
ID14
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P62399, Sequence view
ID 15 : 50S RIBOSOMAL PROTEIN L6
Image
Description50S RIBOSOMAL PROTEIN L6
Typepolypeptide(L)
Formula weight18801.766 Da
Number of molecules1
ID15
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0AG55, Sequence view
ID 16 : 50S RIBOSOMAL PROTEIN L9
Image
Description50S RIBOSOMAL PROTEIN L9
Typepolypeptide(L)
Formula weight15789.174 Da
Number of molecules1
ID16
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7R1, Sequence view
ID 17 : 50S RIBOSOMAL PROTEIN L11
Image
Description50S RIBOSOMAL PROTEIN L11
Typepolypeptide(L)
Formula weight14763.286 Da
Number of molecules1
ID17
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7J7, Sequence view
ID 18 : 50S RIBOSOMAL PROTEIN L13
Image
Description50S RIBOSOMAL PROTEIN L13
Typepolypeptide(L)
Formula weight15822.503 Da
Number of molecules1
ID18
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0AA10, Sequence view
ID 19 : 50S RIBOSOMAL PROTEIN L14
Image
Description50S RIBOSOMAL PROTEIN L14
Typepolypeptide(L)
Formula weight13320.821 Da
Number of molecules1
ID19
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0ADY3, Sequence view
ID 20 : 50S RIBOSOMAL PROTEIN L15
Image
Description50S RIBOSOMAL PROTEIN L15
Typepolypeptide(L)
Formula weight15008.598 Da
Number of molecules1
ID20
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P02413, Sequence view
ID 21 : 50S RIBOSOMAL PROTEIN L16
Image
Description50S RIBOSOMAL PROTEIN L16
Typepolypeptide(L)
Formula weight15312.394 Da
Number of molecules1
ID21
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0ADY7, Sequence view
ID 22 : 50S RIBOSOMAL PROTEIN L17
Image
Description50S RIBOSOMAL PROTEIN L17
Typepolypeptide(L)
Formula weight14393.774 Da
Number of molecules1
ID22
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0AG44, Sequence view
ID 23 : 50S RIBOSOMAL PROTEIN L18
Image
Description50S RIBOSOMAL PROTEIN L18
Typepolypeptide(L)
Formula weight12794.793 Da
Number of molecules1
ID23
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0C018, Sequence view
ID 24 : 50S RIBOSOMAL PROTEIN L19
Image
Description50S RIBOSOMAL PROTEIN L19
Typepolypeptide(L)
Formula weight13028.207 Da
Number of molecules1
ID24
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7K6, Sequence view
ID 25 : 50S RIBOSOMAL PROTEIN L20
Image
Description50S RIBOSOMAL PROTEIN L20
Typepolypeptide(L)
Formula weight13396.962 Da
Number of molecules1
ID25
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7L3, Sequence view
ID 26 : 50S RIBOSOMAL PROTEIN L21
Image
Description50S RIBOSOMAL PROTEIN L21
Typepolypeptide(L)
Formula weight11586.485 Da
Number of molecules1
ID26
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0AG48, Sequence view
ID 27 : 50S RIBOSOMAL PROTEIN L22
Image
Description50S RIBOSOMAL PROTEIN L22
Typepolypeptide(L)
Formula weight12253.464 Da
Number of molecules1
ID27
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P61175, Sequence view
ID 28 : 50S RIBOSOMAL PROTEIN L23
Image
Description50S RIBOSOMAL PROTEIN L23
Typepolypeptide(L)
Formula weight11093.154 Da
Number of molecules1
ID28
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0ADZ0, Sequence view
ID 29 : 50S RIBOSOMAL PROTEIN L24
Image
Description50S RIBOSOMAL PROTEIN L24
Typepolypeptide(L)
Formula weight11078.988 Da
Number of molecules1
ID29
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P60624, Sequence view
ID 30 : 50S RIBOSOMAL PROTEIN L25
Image
Description50S RIBOSOMAL PROTEIN L25
Typepolypeptide(L)
Formula weight10713.566 Da
Number of molecules1
ID30
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P68919, Sequence view
ID 31 : 50S RIBOSOMAL PROTEIN L27
Image
Description50S RIBOSOMAL PROTEIN L27
Typepolypeptide(L)
Formula weight9015.426 Da
Number of molecules1
ID31
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7L8, Sequence view
ID 32 : 50S RIBOSOMAL PROTEIN L29
Image
Description50S RIBOSOMAL PROTEIN L29
Typepolypeptide(L)
Formula weight7286.531 Da
Number of molecules1
ID32
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7M6, Sequence view
ID 33 : 50S RIBOSOMAL PROTEIN L30
Image
Description50S RIBOSOMAL PROTEIN L30
Typepolypeptide(L)
Formula weight6423.682 Da
Number of molecules1
ID33
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0AG51, Sequence view
ID 34 : 50S RIBOSOMAL PROTEIN L31
Image
Description50S RIBOSOMAL PROTEIN L31
Typepolypeptide(L)
Formula weight7887.165 Da
Number of molecules1
ID34
SourceMethod: Isolated from a genetically manipulated source
Gene: MRE600, ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A7M9, Sequence view
ID 35 : MAGNESIUM ION
Image
DescriptionMAGNESIUM ION
Typenon-polymer
Formula weight24.305 Da
Number of molecules111
ID35
SourceMethod: Obtained synthetically
ID 36 : water
Image
Descriptionwater
Typewater
Formula weight18.015 Da
Number of molecules512
ID36
SourceMethod: Isolated from a natural source
Sample
Assembly
Aggregation statePARTICLE
NameSRP BOUND TO 70S RNCS
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample support
DetailsCARBON
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Electron gun
Accelerating voltage300 kV
Lens
ModeBRIGHT FIELD
Processing
2D projection selection
Software nameSPIDER
Single particle entity
Symmetry typeASYMMETRIC
Refine
Refine idELECTRON MICROSCOPY
Ls d res high8.0 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high8.0
Solvent atoms512
Total atoms95358
Ligand atoms111
Nucleic acid atoms65092
Protein atoms29643
Download
PDB format
Allpdb2j28.ent.gz
pdb2j28.ent (uncompressed file)
Header onlypdb2j28.ent.gz
mmCIF format
mmCIF2j28.cif.gz
XML format
All2j28.xml.gz
No-atom2j28-noatom.xml.gz
Ext-atom2j28-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.8 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.3 MB