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E.Coli 70s Ribosome Stalled During Translation Of Tnac Leader Peptide.

by single particle reconstruction, at 5.8 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1657, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1657, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4v5h
TitleE.Coli 70s Ribosome Stalled During Translation Of Tnac Leader Peptide.
DescriptorRibosome
KeywordsRIBOSOME, RIBOSOMAL PROTEIN, RIBONUCLEOPROTEIN, NUCLEOTIDE-BINDING, PROTEIN BIOSYNTHESIS, TRANSLATION, ZINC-FINGER, TNAC, 70S RIBOSOME, STALLING
AuthorsSeidelt, B., Innis, C.A., Wilson, D.N., Gartmann, M., Armache, J., Villa, E., Trabuco, L.G., Becker, T., Mielke, T., Schulten, K., Steitz, T.A., Beckmann, R.
DateDeposition: 2009-10-26, Release: 2014-07-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Compound detailsTHERE IS EXPECTED TO BE A LINK BETWEEN ATOM O3' OF ADENINE AV and BV 76OM O OF ALA Z2. THISAI and BZ TER BOND OF THE NASCENT CHAIN WITH THE TRNA IN THE P-SITE.
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1657, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1657, Image by UCSF CHIMERA

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EMDB-1657

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Article
Citation - primary
ArticleScience, Vol. 326, Issue 5958, Page 1412-5, Year 2009
TitleStructural insight into nascent polypeptide chain-mediated translational stalling.
AuthorsBirgit Seidelt, C Axel Innis, Daniel N Wilson, Marco Gartmann, Jean-Paul Armache, Elizabeth Villa, Leonardo G Trabuco, Thomas Becker, Thorsten Mielke, Klaus Schulten, Thomas A Steitz, Roland Beckmann
Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department for Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
KeywordsBinding Sites, Cryoelectron Microscopy, Escherichia coli (genetics), Escherichia coli Proteins (chemistry), Gene Expression Regulation, Bacterial, Image Processing, Computer-Assisted, Models, Biological, Models, Molecular, Operon, Peptidyl Transferases (metabolism, 2.3.2.12), Protein Biosynthesis, Protein Conformation, RNA-Binding Proteins (chemistry), Ribosomal Proteins (chemistry), Ribosomes (metabolism), Tryptophanase (biosynthesis, 4.1.99.1), rplV protein, E coli, tnaC protein, E coli
LinksDOI: 10.1126/science.1177662, PubMed: 19933110, PMC: PMC2920484
Components
ID 1 : 16S RIBOSOMAL RNA
Image
Description16S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight495927.719 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI

LinksGenBank: 54791136, Sequence view
ID 2 : 30S RIBOSOMAL PROTEIN S2
Image
Description30S RIBOSOMAL PROTEIN S2
Typepolypeptide(L)
FragmentRESIDUES 9-226
Formula weight24253.943 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7V0, Sequence view
ID 3 : 30S RIBOSOMAL PROTEIN S3
Image
Description30S RIBOSOMAL PROTEIN S3
Typepolypeptide(L)
FragmentRESIDUES 2-207
Formula weight23078.785 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7V3, Sequence view
ID 4 : 30S RIBOSOMAL PROTEIN S4
Image
Description30S RIBOSOMAL PROTEIN S4
Typepolypeptide(L)
Formula weight23383.002 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7V8, Sequence view
ID 5 : 30S RIBOSOMAL PROTEIN S5
Image
Description30S RIBOSOMAL PROTEIN S5
Typepolypeptide(L)
FragmentRESIDUES 10-159
Formula weight15804.282 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7W1, Sequence view
ID 6 : 30S RIBOSOMAL PROTEIN S6
Image
Description30S RIBOSOMAL PROTEIN S6
Typepolypeptide(L)
Fragment1-100
Formula weight11669.371 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P02358, Sequence view
ID 7 : 30S RIBOSOMAL PROTEIN S7
Image
Description30S RIBOSOMAL PROTEIN S7
Typepolypeptide(L)
FragmentRESIDUES 3-152
Formula weight16764.406 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P02359, Sequence view
ID 8 : 30S RIBOSOMAL PROTEIN S8
Image
Description30S RIBOSOMAL PROTEIN S8
Typepolypeptide(L)
Formula weight14015.361 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7W7, Sequence view
ID 9 : 30S RIBOSOMAL PROTEIN S9
Image
Description30S RIBOSOMAL PROTEIN S9
Typepolypeptide(L)
FragmentRESIDUES 4-130
Formula weight14554.882 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7X3, Sequence view
ID 10 : 30S RIBOSOMAL PROTEIN S10
Image
Description30S RIBOSOMAL PROTEIN S10
Typepolypeptide(L)
FragmentRESIDUES 5-102
Formula weight11196.988 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7R5, Sequence view
ID 11 : 30S RIBOSOMAL PROTEIN S11
Image
Description30S RIBOSOMAL PROTEIN S11
Typepolypeptide(L)
FragmentRESIDUES 13-129
Formula weight12487.200 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7R9, Sequence view
ID 12 : 30S RIBOSOMAL PROTEIN S12
Image
Description30S RIBOSOMAL PROTEIN S12
Typepolypeptide(L)
Formula weight13636.961 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7S3, Sequence view
ID 13 : 30S RIBOSOMAL PROTEIN S13
Image
Description30S RIBOSOMAL PROTEIN S13
Typepolypeptide(L)
FragmentRESIDUES 2-114
Formula weight12528.639 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7S9, Sequence view
ID 14 : 30S RIBOSOMAL PROTEIN S14
Image
Description30S RIBOSOMAL PROTEIN S14
Typepolypeptide(L)
Formula weight11028.997 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG59, Sequence view
ID 15 : 30S RIBOSOMAL PROTEIN S15
Image
Description30S RIBOSOMAL PROTEIN S15
Typepolypeptide(L)
FragmentRESIDUES 2-89
Formula weight10188.687 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: Q8X9M2, Sequence view
ID 16 : 30S RIBOSOMAL PROTEIN S16
Image
Description30S RIBOSOMAL PROTEIN S16
Typepolypeptide(L)
FragmentRESIDUES 1-80
Formula weight9065.417 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7T3, Sequence view
ID 17 : 30S RIBOSOMAL PROTEIN S17
Image
Description30S RIBOSOMAL PROTEIN S17
Typepolypeptide(L)
FragmentRESIDUES 4-83
Formula weight9263.946 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG63, Sequence view
ID 18 : 30S RIBOSOMAL PROTEIN S18
Image
Description30S RIBOSOMAL PROTEIN S18
Typepolypeptide(L)
FragmentRESIDUES 20-74
Formula weight6466.477 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7T7, Sequence view
ID 19 : 30S RIBOSOMAL PROTEIN S19
Image
Description30S RIBOSOMAL PROTEIN S19
Typepolypeptide(L)
FragmentRESIDUES 3-81
Formula weight9057.626 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7U3, Sequence view
ID 20 : 30S RIBOSOMAL PROTEIN S20
Image
Description30S RIBOSOMAL PROTEIN S20
Typepolypeptide(L)
FragmentRESIDUES 3-87
Formula weight9506.190 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7U7, Sequence view
ID 21 : 30S RIBOSOMAL PROTEIN S21
Image
Description30S RIBOSOMAL PROTEIN S21
Typepolypeptide(L)
FragmentRESIDUES 4-54
Formula weight6067.081 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P68679, Sequence view
ID 22 : P-SITE TRNA
Image
DescriptionP-SITE TRNA
Typepolyribonucleotide
Formula weight24890.803 Da
Number of molecules2
ID22
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksGenBank: 54791136, GenBank: 38859724, Sequence view
ID 23 : MRNA
Image
DescriptionMRNA
Typepolyribonucleotide
Formula weight3497.194 Da
Number of molecules2
ID23
SourceMethod: Obtained synthetically
LinksSequence view
ID 24 : POLY-ALA NASCENT CHAIN
Image
DescriptionPOLY-ALA NASCENT CHAIN
Typepolypeptide(L)
Formula weight1439.571 Da
Number of molecules2
ID24
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksSequence view
ID 25 : 50S RIBOSOMAL PROTEIN L28
Image
Description50S RIBOSOMAL PROTEIN L28
Typepolypeptide(L)
Formula weight8896.354 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7M2, Sequence view
ID 26 : 50S RIBOSOMAL PROTEIN L29
Image
Description50S RIBOSOMAL PROTEIN L29
Typepolypeptide(L)
Formula weight7286.464 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7M6, Sequence view
ID 27 : 50S RIBOSOMAL PROTEIN L30
Image
Description50S RIBOSOMAL PROTEIN L30
Typepolypeptide(L)
Formula weight6423.625 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG51, Sequence view
ID 28 : 50S RIBOSOMAL PROTEIN L32
Image
Description50S RIBOSOMAL PROTEIN L32
Typepolypeptide(L)
Formula weight6332.249 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7N4, Sequence view
ID 29 : 50S RIBOSOMAL PROTEIN L33
Image
Description50S RIBOSOMAL PROTEIN L33
Typepolypeptide(L)
Formula weight5814.842 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7N9, Sequence view
ID 30 : 50S RIBOSOMAL PROTEIN L1
Image
Description50S RIBOSOMAL PROTEIN L1
Typepolypeptide(L)
Formula weight24765.660 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7L0, Sequence view
ID 31 : 50S RIBOSOMAL PROTEIN L34
Image
Description50S RIBOSOMAL PROTEIN L34
Typepolypeptide(L)
Formula weight5397.463 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7P5, Sequence view
ID 32 : 50S RIBOSOMAL PROTEIN L35
Image
Description50S RIBOSOMAL PROTEIN L35
Typepolypeptide(L)
Formula weight7181.835 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7Q1, Sequence view
ID 33 : 50S RIBOSOMAL PROTEIN L36
Image
Description50S RIBOSOMAL PROTEIN L36
Typepolypeptide(L)
Formula weight4377.390 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7Q6, Sequence view
ID 34 : 5S RIBOSOMAL RNA
Image
Description5S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight37848.555 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksGenBank: 38859724, Sequence view
ID 35 : 23S RIBOSOMAL RNA
Image
Description23S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight941306.188 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksGenBank: 38859724, Sequence view
ID 36 : 50S RIBOSOMAL PROTEIN L2
Image
Description50S RIBOSOMAL PROTEIN L2
Typepolypeptide(L)
Formula weight29663.244 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60422, Sequence view
ID 37 : 50S RIBOSOMAL PROTEIN L3
Image
Description50S RIBOSOMAL PROTEIN L3
Typepolypeptide(L)
Formula weight22277.535 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60438, Sequence view
ID 38 : 50S RIBOSOMAL PROTEIN L4
Image
Description50S RIBOSOMAL PROTEIN L4
Typepolypeptide(L)
Formula weight22121.566 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60723, Sequence view
ID 39 : 50S RIBOSOMAL PROTEIN L5
Image
Description50S RIBOSOMAL PROTEIN L5
Typepolypeptide(L)
Formula weight20202.416 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P62399, Sequence view
ID 40 : 50S RIBOSOMAL PROTEIN L6
Image
Description50S RIBOSOMAL PROTEIN L6
Typepolypeptide(L)
Formula weight18801.598 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG55, Sequence view
ID 41 : 50S RIBOSOMAL PROTEIN L9
Image
Description50S RIBOSOMAL PROTEIN L9
Typepolypeptide(L)
Formula weight15789.020 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7R1, Sequence view
ID 42 : 50S RIBOSOMAL PROTEIN L11
Image
Description50S RIBOSOMAL PROTEIN L11
Typepolypeptide(L)
Formula weight14763.165 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7J7, Sequence view
ID 43 : 50S RIBOSOMAL PROTEIN L13
Image
Description50S RIBOSOMAL PROTEIN L13
Typepolypeptide(L)
Formula weight16050.606 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AA10, Sequence view
ID 44 : 50S RIBOSOMAL PROTEIN L14
Image
Description50S RIBOSOMAL PROTEIN L14
Typepolypeptide(L)
Formula weight13352.778 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0ADY3, Sequence view
ID 45 : 50S RIBOSOMAL PROTEIN L15
Image
Description50S RIBOSOMAL PROTEIN L15
Typepolypeptide(L)
FragmentRESIDUES 2-144
Formula weight14877.273 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P02413, Sequence view
ID 46 : 50S RIBOSOMAL PROTEIN L16
Image
Description50S RIBOSOMAL PROTEIN L16
Typepolypeptide(L)
Formula weight15312.269 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0ADY7, Sequence view
ID 47 : 50S RIBOSOMAL PROTEIN L17
Image
Description50S RIBOSOMAL PROTEIN L17
Typepolypeptide(L)
Formula weight13721.938 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG44, Sequence view
ID 48 : 50S RIBOSOMAL PROTEIN L18
Image
Description50S RIBOSOMAL PROTEIN L18
Typepolypeptide(L)
FragmentRESIDUES 2-117
Formula weight12663.471 Da
Number of molecules1
ID48
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0C018, Sequence view
ID 49 : 50S RIBOSOMAL PROTEIN L19
Image
Description50S RIBOSOMAL PROTEIN L19
Typepolypeptide(L)
Formula weight13028.082 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7K6, Sequence view
ID 50 : 50S RIBOSOMAL PROTEIN L20
Image
Description50S RIBOSOMAL PROTEIN L20
Typepolypeptide(L)
Formula weight13396.828 Da
Number of molecules1
ID50
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7L3, Sequence view
ID 51 : 50S RIBOSOMAL PROTEIN L21
Image
Description50S RIBOSOMAL PROTEIN L21
Typepolypeptide(L)
Formula weight11586.374 Da
Number of molecules1
ID51
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG48, Sequence view
ID 52 : 50S RIBOSOMAL PROTEIN L22
Image
Description50S RIBOSOMAL PROTEIN L22
Typepolypeptide(L)
Formula weight12253.359 Da
Number of molecules1
ID52
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P61175, Sequence view
ID 53 : 50S RIBOSOMAL PROTEIN L23
Image
Description50S RIBOSOMAL PROTEIN L23
Typepolypeptide(L)
Formula weight10546.472 Da
Number of molecules1
ID53
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0ADZ0, Sequence view
ID 54 : 50S RIBOSOMAL PROTEIN L24
Image
Description50S RIBOSOMAL PROTEIN L24
Typepolypeptide(L)
Formula weight11078.874 Da
Number of molecules1
ID54
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60624, Sequence view
ID 55 : 50S RIBOSOMAL PROTEIN L25
Image
Description50S RIBOSOMAL PROTEIN L25
Typepolypeptide(L)
Formula weight10713.465 Da
Number of molecules1
ID55
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P68919, Sequence view
ID 56 : 50S RIBOSOMAL PROTEIN L27
Image
Description50S RIBOSOMAL PROTEIN L27
Typepolypeptide(L)
FragmentRESIDUES 7-85
Formula weight8476.680 Da
Number of molecules1
ID56
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7L8, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameTNAC STALLED 70S RIBOSOME WITH P-SITE TRNA.
Buffer
Name50 MM TRIS-HCL PH 8.0, 10MM MG-ACETATE, 50MM KCL, 10MM NH4CL, 2MM EGTA, 2MM L-TRYPTOPHAN, 10 MM DTT
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsCRYOGEN- ETHANE,
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 38900 X, Nominal: 39000 X
CsNominal: 2.26 mm
Nominal defocusMax: 3000 nm, Min: 1000 nm
Specimen holder
Temperature95 Kelvin
Detector
TypeKODAK SO163
Image scans
Number digital images128
Processing
2D projection selection
Number of particles263000
Software nameSPIDER
3D reconstruction
CTF correction methodDEFOCUS GROUP VOLUMES
MethodPROJECTION MATCHING
Resolution5.8 A
3D fitting
MethodMDFF
Refinement ProtocolFLEXIBLE FITTING
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID3FIH,3FIK
Refine
Refine idELECTRON MICROSCOPY
Ls d res high5.80 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high5.80
Total atoms53336
Nucleic acid atoms34716
Protein atoms18620
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PDB format
Allpdb4v5h.ent.gz
pdb4v5h.ent (uncompressed file)
Header onlypdb4v5h.ent.gz
mmCIF format
mmCIF4v5h.cif.gz
XML format
All4v5h.xml.gz
No-atom4v5h-noatom.xml.gz
Ext-atom4v5h-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.2 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 1.3 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 3.8 MB