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tRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)

by single particle reconstruction, at 7.6 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1799, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4v5n
TitletRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)
Descriptor70S ribosome
KeywordsRIBOSOME, TRANSLATION, ELONGATION CYCLE, TRNA TRANSLOCATION
AuthorsRatje, A.H., Loerke, J., Mikolajka, A., Bruenner, M., Hildebrand, P.W., Starosta, A.L., Doenhoefer, A., Connell, S.R., Fucini, P., Mielke, T., Whitford, P.C., Onuchic, J.N., Yu, Y., Sanbonmatsu, K.Y., Hartmann, R.K., Penczek, P.A., Wilson, D.N., Spahn, C.M.T.
DateDeposition: 2010-10-21, Release: 2014-07-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Sequence detailsCHAIN V: MRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE CHAIN X: TRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1799, Image by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1799

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Article
Citation - primary
ArticleNature, Vol. 468, Issue 7324, Page 713-6, Year 2010
TitleHead swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
AuthorsAndreas H Ratje, Justus Loerke, Aleksandra Mikolajka, Matthias Brünner, Peter W Hildebrand, Agata L Starosta, Alexandra Dönhöfer, Sean R Connell, Paola Fucini, Thorsten Mielke, Paul C Whitford, José N Onuchic, Yanan Yu, Karissa Y Sanbonmatsu, Roland K Hartmann, Pawel A Penczek, Daniel N Wilson, Christian M T Spahn
Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117-Berlin, Germany.
KeywordsBinding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Guanosine Diphosphate (chemistry, 146-91-8), Models, Molecular, Movement, Peptide Elongation Factor G (chemistry), Protein Biosynthesis, Protein Conformation, Protein Subunits (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosome Subunits, Small, Bacterial (chemistry), Thermus thermophilus (chemistry)
LinksDOI: 10.1038/nature09547, PubMed: 21124459, PMC: PMC3272701
Components
ID 1 : 16S RRNA
Image
Description16S RRNA
Typepolyribonucleotide
Formula weight493958.281 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksGenBank: 55979969, Sequence view
ID 2 : 30S RIBOSOMAL PROTEIN S2
Image
Description30S RIBOSOMAL PROTEIN S2
Typepolypeptide(L)
Formula weight29317.703 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80371, Sequence view
ID 3 : 30S RIBOSOMAL PROTEIN S3
Image
Description30S RIBOSOMAL PROTEIN S3
Typepolypeptide(L)
Formula weight26751.076 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80372, Sequence view
ID 4 : 30S RIBOSOMAL PROTEIN S4
Image
Description30S RIBOSOMAL PROTEIN S4
Typepolypeptide(L)
Formula weight24373.447 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80373, Sequence view
ID 5 : 30S RIBOSOMAL PROTEIN S5
Image
Description30S RIBOSOMAL PROTEIN S5
Typepolypeptide(L)
Formula weight17583.416 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHQ5, Sequence view
ID 6 : 30S RIBOSOMAL PROTEIN S6
Image
Description30S RIBOSOMAL PROTEIN S6
Typepolypeptide(L)
Formula weight11988.753 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SLP8, Sequence view
ID 7 : 30S RIBOSOMAL PROTEIN S7
Image
Description30S RIBOSOMAL PROTEIN S7
Typepolypeptide(L)
Formula weight18050.973 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P17291, Sequence view
ID 8 : 30S RIBOSOMAL PROTEIN S8
Image
Description30S RIBOSOMAL PROTEIN S8
Typepolypeptide(L)
Formula weight15868.570 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHQ2, Sequence view
ID 9 : 30S RIBOSOMAL PROTEIN S9
Image
Description30S RIBOSOMAL PROTEIN S9
Typepolypeptide(L)
Formula weight14410.614 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80374, Sequence view
ID 10 : 30S RIBOSOMAL PROTEIN S10
Image
Description30S RIBOSOMAL PROTEIN S10
Typepolypeptide(L)
Formula weight11954.968 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHN7, Sequence view
ID 11 : 30S RIBOSOMAL PROTEIN S11
Image
Description30S RIBOSOMAL PROTEIN S11
Typepolypeptide(L)
Formula weight13737.868 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80376, Sequence view
ID 12 : 30S RIBOSOMAL PROTEIN S12
Image
Description30S RIBOSOMAL PROTEIN S12
Typepolypeptide(L)
Formula weight14637.384 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHN3, Sequence view
ID 13 : 30S RIBOSOMAL PROTEIN S13
Image
Description30S RIBOSOMAL PROTEIN S13
Typepolypeptide(L)
Formula weight14338.861 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80377, Sequence view
ID 14 : 30S RIBOSOMAL PROTEIN S14 TYPE Z
Image
Description30S RIBOSOMAL PROTEIN S14 TYPE Z
Typepolypeptide(L)
Formula weight7158.725 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHQ1, Sequence view
ID 15 : 30S RIBOSOMAL PROTEIN S15
Image
Description30S RIBOSOMAL PROTEIN S15
Typepolypeptide(L)
Formula weight10578.407 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SJ76, Sequence view
ID 16 : 30S RIBOSOMAL PROTEIN S16
Image
Description30S RIBOSOMAL PROTEIN S16
Typepolypeptide(L)
Formula weight10409.983 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SJH3, Sequence view
ID 17 : 30S RIBOSOMAL PROTEIN S17
Image
Description30S RIBOSOMAL PROTEIN S17
Typepolypeptide(L)
Formula weight12325.655 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHP7, Sequence view
ID 18 : 30S RIBOSOMAL PROTEIN S18
Image
Description30S RIBOSOMAL PROTEIN S18
Typepolypeptide(L)
Formula weight10258.299 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SLQ0, Sequence view
ID 19 : 30S RIBOSOMAL PROTEIN S19
Image
Description30S RIBOSOMAL PROTEIN S19
Typepolypeptide(L)
Formula weight10605.464 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHP2, Sequence view
ID 20 : 30S RIBOSOMAL PROTEIN S20
Image
Description30S RIBOSOMAL PROTEIN S20
Typepolypeptide(L)
Formula weight11736.143 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80380, Sequence view
ID 21 : 30S RIBOSOMAL PROTEIN THX
Image
Description30S RIBOSOMAL PROTEIN THX
Typepolypeptide(L)
Formula weight3350.030 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SIH3, Sequence view
ID 22 : TRNA
Image
DescriptionTRNA
Typepolyribonucleotide
Formula weight24802.785 Da
Number of molecules1
ID22
DetailsTRNA WAS COPURIFIED WITH 70S RIBOSOMES
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksSequence view
ID 23 : MRNA
Image
DescriptionMRNA
Typepolyribonucleotide
Formula weight3476.122 Da
Number of molecules1
ID23
DetailsMRNA WAS COPURIFIED WITH 70S RIBOSOMES
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksSequence view
ID 24 : ELONGATION FACTOR G
Image
DescriptionELONGATION FACTOR G
Typepolypeptide(L)
Formula weight76977.102 Da
Number of molecules1
ID24
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: HB8, 27634, ID:300852, THERMUS THERMOPHILUS
Host: ID:469008, ESCHERICHIA COLI

, BL21(DE3)
Plasmid name: PET-46 EK/LIC
LinksUniProt: Q5SHN5, Sequence view
ID 25 : 50S RIBOSOMAL PROTEIN L27
Image
Description50S RIBOSOMAL PROTEIN L27
Typepolypeptide(L)
Formula weight9529.074 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60493, Sequence view
ID 26 : 50S RIBOSOMAL PROTEIN L28
Image
Description50S RIBOSOMAL PROTEIN L28
Typepolypeptide(L)
Formula weight11004.160 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60494, Sequence view
ID 27 : TL5
Image
Description50S RIBOSOMAL PROTEIN L29
Typepolypeptide(L)
Formula weight8670.258 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP6, Sequence view
ID 28 : 50S RIBOSOMAL PROTEIN L30
Image
Description50S RIBOSOMAL PROTEIN L30
Typepolypeptide(L)
Formula weight6799.126 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ6, Sequence view
ID 29 : 50S RIBOSOMAL PROTEIN L31
Image
Description50S RIBOSOMAL PROTEIN L31
Typepolypeptide(L)
Formula weight8300.543 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SJE1, Sequence view
ID 30 : 50S RIBOSOMAL PROTEIN L32
Image
Description50S RIBOSOMAL PROTEIN L32
Typepolypeptide(L)
Formula weight6722.050 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P80339, Sequence view
ID 31 : 50S RIBOSOMAL PROTEIN L33
Image
Description50S RIBOSOMAL PROTEIN L33
Typepolypeptide(L)
Formula weight6632.896 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P35871, Sequence view
ID 32 : 50S RIBOSOMAL PROTEIN L34
Image
Description50S RIBOSOMAL PROTEIN L34
Typepolypeptide(L)
Formula weight6132.449 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P80340, Sequence view
ID 33 : 50S RIBOSOMAL PROTEIN L35
Image
Description50S RIBOSOMAL PROTEIN L35
Typepolypeptide(L)
Formula weight7506.178 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SKU1, Sequence view
ID 34 : RIBOSOMAL PROTEIN B
Image
Description50S RIBOSOMAL PROTEIN L36
Typepolypeptide(L)
Formula weight4435.411 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHR2, Sequence view
ID 35 : 23S RIBOSOMAL RNA
Image
Description23S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight947935.438 Da
Number of molecules1
ID35
DetailsCHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksGenBank: 55979969, Sequence view
ID 36 : 5S RIBOSOMAL RNA
Image
Description5S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight39540.617 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksGenBank: 55979969, Sequence view
ID 37 : 50S RIBOSOMAL PROTEIN L1
Image
Description50S RIBOSOMAL PROTEIN L1
Typepolypeptide(L)
Formula weight24872.721 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SLP7, Sequence view
ID 38 : 50S RIBOSOMAL PROTEIN L2
Image
Description50S RIBOSOMAL PROTEIN L2
Typepolypeptide(L)
Formula weight30532.551 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60405, Sequence view
ID 39 : 50S RIBOSOMAL PROTEIN L3
Image
Description50S RIBOSOMAL PROTEIN L3
Typepolypeptide(L)
Formula weight22450.213 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHN8, Sequence view
ID 40 : L1E
Image
Description50S RIBOSOMAL PROTEIN L4
Typepolypeptide(L)
Formula weight23271.914 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHN9, Sequence view
ID 41 : 50S RIBOSOMAL PROTEIN L5
Image
Description50S RIBOSOMAL PROTEIN L5
Typepolypeptide(L)
Formula weight21061.596 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ0, Sequence view
ID 42 : 50S RIBOSOMAL PROTEIN L6
Image
Description50S RIBOSOMAL PROTEIN L6
Typepolypeptide(L)
Formula weight19568.926 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ3, Sequence view
ID 43 : 50S RIBOSOMAL PROTEIN L11
Image
Description50S RIBOSOMAL PROTEIN L11
Typepolypeptide(L)
Formula weight15526.111 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SLP6, Sequence view
ID 44 : 50S RIBOSOMAL PROTEIN L7/L12
Image
Description50S RIBOSOMAL PROTEIN L7/L12
Typepolypeptide(L)
Formula weight12309.155 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:83333
Organism scientific: ESCHERICHIA COLI
Strain: K-12
LinksUniProt: P0A7K2, Sequence view
ID 45 : 50S RIBOSOMAL PROTEIN L13
Image
Description50S RIBOSOMAL PROTEIN L13
Typepolypeptide(L)
Formula weight15927.903 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60488, Sequence view
ID 46 : 50S RIBOSOMAL PROTEIN L14
Image
Description50S RIBOSOMAL PROTEIN L14
Typepolypeptide(L)
Formula weight13323.612 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP8, Sequence view
ID 47 : 50S RIBOSOMAL PROTEIN L15
Image
Description50S RIBOSOMAL PROTEIN L15
Typepolypeptide(L)
Formula weight16319.142 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ7, Sequence view
ID 48 : 50S RIBOSOMAL PROTEIN L16
Image
Description50S RIBOSOMAL PROTEIN L16
Typepolypeptide(L)
Formula weight15993.909 Da
Number of molecules1
ID48
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60489, Sequence view
ID 49 : 50S RIBOSOMAL PROTEIN L17
Image
Description50S RIBOSOMAL PROTEIN L17
Typepolypeptide(L)
Formula weight13750.148 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q9Z9H5, Sequence view
ID 50 : TL24
Image
Description50S RIBOSOMAL PROTEIN L18
Typepolypeptide(L)
Formula weight12639.845 Da
Number of molecules1
ID50
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ4, Sequence view
ID 51 : 50S RIBOSOMAL PROTEIN L19
Image
Description50S RIBOSOMAL PROTEIN L19
Typepolypeptide(L)
Formula weight17188.830 Da
Number of molecules1
ID51
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60490, Sequence view
ID 52 : 50S RIBOSOMAL PROTEIN L20
Image
Description50S RIBOSOMAL PROTEIN L20
Typepolypeptide(L)
Formula weight13779.275 Da
Number of molecules1
ID52
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60491, Sequence view
ID 53 : 50S RIBOSOMAL PROTEIN L21
Image
Description50S RIBOSOMAL PROTEIN L21
Typepolypeptide(L)
Formula weight11069.153 Da
Number of molecules1
ID53
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60492, Sequence view
ID 54 : 50S RIBOSOMAL PROTEIN L22
Image
Description50S RIBOSOMAL PROTEIN L22
Typepolypeptide(L)
Formula weight12808.055 Da
Number of molecules1
ID54
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP3, Sequence view
ID 55 : 50S RIBOSOMAL PROTEIN L23
Image
Description50S RIBOSOMAL PROTEIN L23
Typepolypeptide(L)
Formula weight10759.808 Da
Number of molecules1
ID55
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP0, Sequence view
ID 56 : 50S RIBOSOMAL PROTEIN L24
Image
Description50S RIBOSOMAL PROTEIN L24
Typepolypeptide(L)
Formula weight12085.611 Da
Number of molecules1
ID56
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP9, Sequence view
ID 57 : TL5
Image
Description50S RIBOSOMAL PROTEIN L25
Typepolypeptide(L)
Formula weight23238.572 Da
Number of molecules1
ID57
SourceMethod: Isolated from a natural source
Src id: 1
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHZ1, Sequence view
ID 58 : FUSIDIC ACID
Image
DescriptionFUSIDIC ACID
Typenon-polymer
Formula weight516.709 Da
Number of molecules1
ID58
SourceMethod: Obtained synthetically
ID 59 : GUANOSINE-5'-DIPHOSPHATE
Image
DescriptionGUANOSINE-5'-DIPHOSPHATE
Typenon-polymer
Formula weight443.201 Da
Number of molecules1
ID59
SourceMethod: Obtained synthetically
Sample
Assembly
Aggregation statePARTICLE
Name70S-EFG-GDP-FA COMPLEX
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- VITROBOT (FEI)
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
DetailsLOW-DOSE
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 65520 X, Nominal: 39000 X
CsNominal: 2.0 mm
Nominal defocusMax: 4000 nm, Min: 2000 nm
Specimen holder
Temperature77 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images677
Processing
2D projection selection
Software nameSPIDER
3D reconstruction
Actual pixel size1.26 A/pix
CTF correction methodDEFOCUS GROUPS
DetailsSUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1799. (DEPOSITION ID: 7584).
MethodMULTIPARTICLE REFINEMENT
Nominal pixel size1.26 A/pix
Resolution7.6 A
3D fitting
MethodMDFIT
Refinement ProtocolX-RAY
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID2WRI,2WRJ
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.60 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.60
Total atoms58624
Ligand atoms65
Nucleic acid atoms34199
Protein atoms24360
Download
PDB format
Allpdb4v5n.ent.gz
pdb4v5n.ent (uncompressed file)
Header onlypdb4v5n.ent.gz
mmCIF format
mmCIF4v5n.cif.gz
XML format
All4v5n.xml.gz
No-atom4v5n-noatom.xml.gz
Ext-atom4v5n-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.1 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 740.2 KB
.webm (WebM/VP8 format), 385.3 KB