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Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome

by single particle reconstruction, at 8.8 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1669, Image by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1811, Image by Jmol

#4: With PDB-3izd, Image by Jmol

#5: Superimposing with EM 3D map: EMDB-1811 (with PDB-3izd), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4v6i
TitleLocalization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome
DescriptorRibosome
KeywordsRIBOSOME, eukaryotic ribosome, homology modeling, de novo modeling, ribosomal proteins, novel ribosomal proteins
AuthorsArmache, J.-P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soeding, J., Westhof, E., Wilson, D.N., Beckmann, R.
DateDeposition: 2010-10-12, Release: 2014-07-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1669, Image by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1811, Image by Jmol

#4: With PDB-3izd, Image by Jmol

#5: Superimposing with EM 3D map: EMDB-1811 (with PDB-3izd), Image by UCSF CHIMERA

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 46, Page 19748-53, Year 2010
TitleCryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
AuthorsJean-Paul Armache, Alexander Jarasch, Andreas M Anger, Elizabeth Villa, Thomas Becker, Shashi Bhushan, Fabrice Jossinet, Michael Habeck, Gülcin Dindar, Sibylle Franckenberg, Viter Marquez, Thorsten Mielke, Michael Thomm, Otto Berninghausen, Birgitta Beatrix, Johannes Söding, Eric Westhof, Daniel N Wilson, Roland Beckmann
Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
KeywordsCryoelectron Microscopy, Crystallography, X-Ray, Escherichia coli (metabolism), Eukaryotic Cells (metabolism), Humans, Models, Molecular, Protein Biosynthesis, RNA, Ribosomal (ultrastructure), Ribosomes (chemistry), Saccharomyces cerevisiae (metabolism), Triticum (metabolism)
LinksDOI: 10.1073/pnas.1009999107, PubMed: 20980660, PMC: PMC2993355
Citation - 1
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 46, Page 19754-9, Year 2010
TitleLocalization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
AuthorsJean-Paul Armache, Alexander Jarasch, Andreas M Anger, Elizabeth Villa, Thomas Becker, Shashi Bhushan, Fabrice Jossinet, Michael Habeck, Gülcin Dindar, Sibylle Franckenberg, Viter Marquez, Thorsten Mielke, Michael Thomm, Otto Berninghausen, Birgitta Beatrix, Johannes Söding, Eric Westhof, Daniel N Wilson, Roland Beckmann
Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
KeywordsCryoelectron Microscopy, Eukaryotic Cells (metabolism), Evolution, Molecular, Models, Molecular, Protein Transport, RNA, Ribosomal (chemistry), Ribosomal Proteins (metabolism), Ribosomes (metabolism), Saccharomyces cerevisiae (metabolism), Species Specificity, Triticum (metabolism)
LinksDOI: 10.1073/pnas.1010005107, PubMed: 20974910, PMC: PMC2993421
Components
ID 1 : 40S ribosomal protein RACK1 (RACK1)
Image
Description40S ribosomal protein RACK1 (RACK1)
Typepolypeptide(L)
Formula weight34841.219 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae

LinksUniProt: P38011, Sequence view
ID 2 : 40S ribosomal protein rpS0 (S2p)
Image
Description40S ribosomal protein rpS0 (S2p)
Typepolypeptide(L)
Formula weight28051.330 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P32905, Sequence view
ID 3 : 40S ribosomal protein rpS3 (S3p)
Image
Description40S ribosomal protein rpS3 (S3p)
Typepolypeptide(L)
Formula weight26542.789 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05750, Sequence view
ID 4 : 40S ribosomal protein rpS4 (S4e)
Image
Description40S ribosomal protein rpS4 (S4e)
Typepolypeptide(L)
Formula weight29469.330 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05753, Sequence view
ID 5 : 40S ribosomal protein rpS9 (S4p)
Image
Description40S ribosomal protein rpS9 (S4p)
Typepolypeptide(L)
Formula weight22487.893 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: O13516, Sequence view
ID 6 : 40S ribosomal protein rpS2 (S5p)
Image
Description40S ribosomal protein rpS2 (S5p)
Typepolypeptide(L)
Formula weight27490.826 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P25443, Sequence view
ID 7 : 40S ribosomal protein rpS7 (S7e)
Image
Description40S ribosomal protein rpS7 (S7e)
Typepolypeptide(L)
Formula weight12273.120 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 8 : 40S ribosomal protein rpS5 (S7p)
Image
Description40S ribosomal protein rpS5 (S7p)
Typepolypeptide(L)
Formula weight25072.600 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P26783, Sequence view
ID 9 : 40S ribosomal protein rpS22 (S8p)
Image
Description40S ribosomal protein rpS22 (S8p)
Typepolypeptide(L)
Formula weight14650.062 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P0C0W1, Sequence view
ID 10 : 40S ribosomal protein rpS16 (S9p)
Image
Description40S ribosomal protein rpS16 (S9p)
Typepolypeptide(L)
Formula weight15877.490 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P40213, Sequence view
ID 11 : 40S ribosomal protein rpS20 (S10p)
Image
Description40S ribosomal protein rpS20 (S10p)
Typepolypeptide(L)
Formula weight13929.044 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P38701, Sequence view
ID 12 : 40S ribosomal protein rpS14 (S11p)
Image
Description40S ribosomal protein rpS14 (S11p)
Typepolypeptide(L)
Formula weight14562.655 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P06367, Sequence view
ID 13 : 40S ribosomal protein rpS23 (S12p)
Image
Description40S ribosomal protein rpS23 (S12p)
Typepolypeptide(L)
Formula weight16073.896 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P32827, Sequence view
ID 14 : 40S ribosomal protein rpS18 (S13p)
Image
Description40S ribosomal protein rpS18 (S13p)
Typepolypeptide(L)
Formula weight17071.641 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P35271, Sequence view
ID 15 : 40S ribosomal protein rpS29 (S14p)
Image
Description40S ribosomal protein rpS29 (S14p)
Typepolypeptide(L)
Formula weight6675.723 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P41057, Sequence view
ID 16 : 40S ribosomal protein rpS13 (S15p)
Image
Description40S ribosomal protein rpS13 (S15p)
Typepolypeptide(L)
Formula weight17059.945 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05756, Sequence view
ID 17 : 40S ribosomal protein rpS17 (S17e)
Image
Description40S ribosomal protein rpS17 (S17e)
Typepolypeptide(L)
Formula weight15820.413 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P02407, Sequence view
ID 18 : 40S ribosomal protein rpS11 (S17p)
Image
Description40S ribosomal protein rpS11 (S17p)
Typepolypeptide(L)
Formula weight17785.934 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P26781, Sequence view
ID 19 : 40S ribosomal protein rpS15 (S19p)
Image
Description40S ribosomal protein rpS15 (S19p)
Typepolypeptide(L)
Formula weight16031.907 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: Q01855, Sequence view
ID 20 : 40S ribosomal protein rpS19 (S19e)
Image
Description40S ribosomal protein rpS19 (S19e)
Typepolypeptide(L)
Formula weight15942.125 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P07280, Sequence view
ID 21 : 40S ribosomal protein rpS21 (S21e)
Image
Description40S ribosomal protein rpS21 (S21e)
Typepolypeptide(L)
Formula weight9758.829 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P0C0V8, Sequence view
ID 22 : 40S ribosomal protein rpS25 (S25e)
Image
Description40S ribosomal protein rpS25 (S25e)
Typepolypeptide(L)
Formula weight12067.272 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: Q3E792, Sequence view
ID 23 : 40S ribosomal protein rpS26 (S26e)
Image
Description40S ribosomal protein rpS26 (S26e)
Typepolypeptide(L)
Formula weight7932.770 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 24 : 40S ribosomal protein rpS27 (S27e)
Image
Description40S ribosomal protein rpS27 (S27e)
Typepolypeptide(L)
Formula weight8893.391 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P35997, Sequence view
ID 25 : 40S ribosomal protein rpS28 (S28e)
Image
Description40S ribosomal protein rpS28 (S28e)
Typepolypeptide(L)
Formula weight7605.847 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: Q3E7X9, Sequence view
ID 26 : 40S ribosomal protein rpS30 (S30e)
Image
Description40S ribosomal protein rpS30 (S30e)
Typepolypeptide(L)
Formula weight7137.541 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: Q12087, Sequence view
ID 27 : Unknown 40S ribosomal protein XS1
Image
DescriptionUnknown 40S ribosomal protein XS1
Typepolypeptide(L)
Formula weight3166.895 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 28 : Unknown 40S ribosomal protein XS2
Image
DescriptionUnknown 40S ribosomal protein XS2
Typepolypeptide(L)
Formula weight2230.741 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 29 : 40S ribosomal protein S24
Image
Description40S ribosomal protein S24
Typepolypeptide(L)
Formula weight15362.848 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P26782, Sequence view
ID 30 : 60S ribosomal protein rpL1 (L1p)
Image
Description60S ribosomal protein rpL1 (L1p)
Typepolypeptide(L)
Formula weight24524.799 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P53030, Sequence view
ID 31 : 60S ribosomal protein rpL2 (L2p)
Image
Description60S ribosomal protein rpL2 (L2p)
Typepolypeptide(L)
Formula weight27463.574 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05736, Sequence view
ID 32 : 60S ribosomal protein rpL3 (L3p)
Image
Description60S ribosomal protein rpL3 (L3p)
Typepolypeptide(L)
Formula weight43907.844 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P14126, Sequence view
ID 33 : 60S ribosomal protein rpL4 (L4p)
Image
Description60S ribosomal protein rpL4 (L4p)
Typepolypeptide(L)
Formula weight39159.125 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P10664, Sequence view
ID 34 : 60S ribosomal protein rpL11 (L5p)
Image
Description60S ribosomal protein rpL11 (L5p)
Typepolypeptide(L)
Formula weight19755.691 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P0C0W9, Sequence view
ID 35 : 60S ribosomal protein rpL6 (L6e)
Image
Description60S ribosomal protein rpL6 (L6e)
Typepolypeptide(L)
Formula weight20000.564 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: Q02326, Sequence view
ID 36 : 60S ribosomal protein rpL9 (L6p)
Image
Description60S ribosomal protein rpL9 (L6p)
Typepolypeptide(L)
Formula weight21605.061 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05738, Sequence view
ID 37 : 60S ribosomal protein rpL8 (L7ae)
Image
Description60S ribosomal protein rpL8 (L7ae)
Typepolypeptide(L)
Formula weight28175.820 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P17076, Sequence view
ID 38 : 60S acidic ribosomal protein rpP0 (L10P)
Image
Description60S acidic ribosomal protein rpP0 (L10P)
Typepolypeptide(L)
Formula weight33749.121 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05317, Sequence view
ID 39 : 60S ribosomal protein rpL12 (L11p)
Image
Description60S ribosomal protein rpL12 (L11p)
Typepolypeptide(L)
Formula weight17850.621 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P17079, Sequence view
ID 40 : 60S ribosomal protein rpL16 (L13p)
Image
Description60S ribosomal protein rpL16 (L13p)
Typepolypeptide(L)
Formula weight22247.227 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P26784, Sequence view
ID 41 : 60S ribosomal protein rpL14 (L14e)
Image
Description60S ribosomal protein rpL14 (L14e)
Typepolypeptide(L)
Formula weight15195.066 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: D6VXT1, Sequence view
ID 42 : 60S ribosomal protein rpL23 (L14p)
Image
Description60S ribosomal protein rpL23 (L14p)
Typepolypeptide(L)
Formula weight14493.950 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P04451, Sequence view
ID 43 : 60S ribosomal protein rpL15 (L15e)
Image
Description60S ribosomal protein rpL15 (L15e)
Typepolypeptide(L)
Formula weight24482.357 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05748, Sequence view
ID 44 : 60S ribosomal protein rpL28 (L15p)
Image
Description60S ribosomal protein rpL28 (L15p)
Typepolypeptide(L)
Formula weight16761.666 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P02406, Sequence view
ID 45 : 60S ribosomal protein rpL18 (L18e)
Image
Description60S ribosomal protein rpL18 (L18e)
Typepolypeptide(L)
Formula weight20609.252 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P07279, Sequence view
ID 46 : 60S ribosomal protein rpL19 (L19e)
Image
Description60S ribosomal protein rpL19 (L19e)
Typepolypeptide(L)
Formula weight21762.316 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05735, Sequence view
ID 47 : 60S ribosomal protein rpL21 (L21e)
Image
Description60S ribosomal protein rpL21 (L21e)
Typepolypeptide(L)
Formula weight18279.266 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: Q02753, Sequence view
ID 48 : 60S ribosomal protein rpL22 (L22e)
Image
Description60S ribosomal protein rpL22 (L22e)
Typepolypeptide(L)
Formula weight13711.359 Da
Number of molecules1
ID48
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05749, Sequence view
ID 49 : 60S ribosomal protein rpL17 (L22p)
Image
Description60S ribosomal protein rpL17 (L22p)
Typepolypeptide(L)
Formula weight19007.621 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05740, Sequence view
ID 50 : 60S ribosomal protein rpL25 (L23p)
Image
Description60S ribosomal protein rpL25 (L23p)
Typepolypeptide(L)
Formula weight15787.612 Da
Number of molecules1
ID50
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P04456, Sequence view
ID 51 : 60S ribosomal protein rpL24 (L24e)
Image
Description60S ribosomal protein rpL24 (L24e)
Typepolypeptide(L)
Formula weight17661.717 Da
Number of molecules1
ID51
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P04449, Sequence view
ID 52 : 60S ribosomal protein rpL26 (L24p)
Image
Description60S ribosomal protein rpL26 (L24p)
Typepolypeptide(L)
Formula weight13837.280 Da
Number of molecules1
ID52
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05743, Sequence view
ID 53 : 60S ribosomal protein rpL27 (L27e)
Image
Description60S ribosomal protein rpL27 (L27e)
Typepolypeptide(L)
Formula weight15568.360 Da
Number of molecules1
ID53
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P0C2H6, Sequence view
ID 54 : 60S ribosomal protein rpL29 (L29e)
Image
Description60S ribosomal protein rpL29 (L29e)
Typepolypeptide(L)
Formula weight6691.884 Da
Number of molecules1
ID54
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05747, Sequence view
ID 55 : 60S ribosomal protein rpL35 (L29p)
Image
Description60S ribosomal protein rpL35 (L29p)
Typepolypeptide(L)
Formula weight13942.640 Da
Number of molecules1
ID55
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P39741, Sequence view
ID 56 : 60S ribosomal protein rpL30 (L30e)
Image
Description60S ribosomal protein rpL30 (L30e)
Typepolypeptide(L)
Formula weight11430.364 Da
Number of molecules1
ID56
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P14120, Sequence view
ID 57 : 60S ribosomal protein rpL7 (L30p)
Image
Description60S ribosomal protein rpL7 (L30p)
Typepolypeptide(L)
Formula weight27686.281 Da
Number of molecules1
ID57
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05737, Sequence view
ID 58 : 60S ribosomal protein rpL31 (L31e)
Image
Description60S ribosomal protein rpL31 (L31e)
Typepolypeptide(L)
Formula weight12980.158 Da
Number of molecules1
ID58
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P0C2H8, Sequence view
ID 59 : 60S ribosomal protein pL32 (L32e)
Image
Description60S ribosomal protein pL32 (L32e)
Typepolypeptide(L)
Formula weight14809.441 Da
Number of molecules1
ID59
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P38061, Sequence view
ID 60 : 60S ribosomal protein rpL34 (L34e)
Image
Description60S ribosomal protein rpL34 (L34e)
Typepolypeptide(L)
Formula weight13343.759 Da
Number of molecules1
ID60
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P87262, Sequence view
ID 61 : 60S ribosomal protein rpL33 (L35ae)
Image
Description60S ribosomal protein rpL33 (L35ae)
Typepolypeptide(L)
Formula weight12177.130 Da
Number of molecules1
ID61
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05744, Sequence view
ID 62 : 60S ribosomal protein rpL36 (L36e)
Image
Description60S ribosomal protein rpL36 (L36e)
Typepolypeptide(L)
Formula weight11151.259 Da
Number of molecules1
ID62
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05745, Sequence view
ID 63 : 60S ribosomal protein rpL43 (L37ae)
Image
Description60S ribosomal protein rpL43 (L37ae)
Typepolypeptide(L)
Formula weight10112.952 Da
Number of molecules1
ID63
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P49631, Sequence view
ID 64 : 60S ribosomal protein rpL37 (L37e)
Image
Description60S ribosomal protein rpL37 (L37e)
Typepolypeptide(L)
Formula weight9877.395 Da
Number of molecules1
ID64
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P49166, Sequence view
ID 65 : 60S ribosomal protein rpL38 (L38e)
Image
Description60S ribosomal protein rpL38 (L38e)
Typepolypeptide(L)
Formula weight8845.561 Da
Number of molecules1
ID65
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P49167, Sequence view
ID 66 : 60S ribosomal protein rpL39 (L39e)
Image
Description60S ribosomal protein rpL39 (L39e)
Typepolypeptide(L)
Formula weight6358.640 Da
Number of molecules1
ID66
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P04650, Sequence view
ID 67 : 60S ribosomal protein rpL40 (L40e)
Image
Description60S ribosomal protein rpL40 (L40e)
Typepolypeptide(L)
Formula weight6032.321 Da
Number of molecules1
ID67
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P0CH08, Sequence view
ID 68 : 60S ribosomal protein rpL41 (L41e)
Image
Description60S ribosomal protein rpL41 (L41e)
Typepolypeptide(L)
Formula weight3354.243 Da
Number of molecules1
ID68
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05746, Sequence view
ID 69 : 60S ribosomal protein rpL42 (L44e)
Image
Description60S ribosomal protein rpL42 (L44e)
Typepolypeptide(L)
Formula weight12246.658 Da
Number of molecules1
ID69
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P02405, Sequence view
ID 70 : Unknown protein
Image
DescriptionUnknown protein
Typepolypeptide(L)
Formula weight1805.216 Da
Number of molecules2
ID70
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 71 : Unknown protein
Image
DescriptionUnknown protein
Typepolypeptide(L)
Formula weight1294.587 Da
Number of molecules1
ID71
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 72 : 60S acidic ribosomal protein rpP11 (P1)
Image
Description60S acidic ribosomal protein rpP11 (P1)
Typepolypeptide(L)
Formula weight10928.809 Da
Number of molecules2
ID72
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05318, Sequence view
ID 73 : 60S acidic ribosomal protein (P2)
Image
Description60S acidic ribosomal protein (P2)
Typepolypeptide(L)
Formula weight10752.715 Da
Number of molecules2
ID73
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P05319, Sequence view
ID 74 : 60S ribosomal protein rpL5 (L18p)
Image
Description60S ribosomal protein rpL5 (L18p)
Typepolypeptide(L)
Formula weight33792.844 Da
Number of molecules1
ID74
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P26321, Sequence view
ID 75 : 60S ribosomal protein rpL13 (L13e)
Image
Description60S ribosomal protein rpL13 (L13e)
Typepolypeptide(L)
Formula weight14485.838 Da
Number of molecules1
ID75
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 76 : 60S ribosomal protein rpL20 (L18ae)
Image
Description60S ribosomal protein rpL20 (L18ae)
Typepolypeptide(L)
Formula weight20148.668 Da
Number of molecules1
ID76
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: Q0JJA0, Sequence view
ID 77 : 60S ribosomal protein rpL10 (L10e)
Image
Description60S ribosomal protein rpL10 (L10e)
Typepolypeptide(L)
Formula weight25410.465 Da
Number of molecules1
ID77
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksUniProt: P41805, Sequence view
ID 78 : 18S rRNA
Image
Description18S rRNA
Typepolyribonucleotide
Formula weight579761.938 Da
Number of molecules1
ID78
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksGenBank: U53879.1, Sequence view
ID 79 : P-SITE TRNA ASP
Image
DescriptionP-SITE TRNA ASP
Typepolyribonucleotide
Formula weight24135.262 Da
Number of molecules1
ID79
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksGenBank: M25599.1, Sequence view
ID 80 : MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')
Image
DescriptionMRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')
Typepolyribonucleotide
Formula weight3498.178 Da
Number of molecules1
ID80
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksSequence view
ID 81 : 25S rRNA
Image
Description25S rRNA
Typepolyribonucleotide
Formula weight1097493.875 Da
Number of molecules1
ID81
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksGenBank: U53879.1, Sequence view
ID 82 : 5.8S rRNA
Image
Description5.8S rRNA
Typepolyribonucleotide
Formula weight50682.922 Da
Number of molecules1
ID82
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksGenBank: U53879.1, Sequence view
ID 83 : 5S rRNA
Image
Description5S rRNA
Typepolyribonucleotide
Formula weight37947.492 Da
Number of molecules1
ID83
SourceMethod: Isolated from a natural source
Src id: 1
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae
LinksGenBank: U53879.1, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Processing
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Resolution8.8 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms28040
Protein atoms28040
Download
PDB format
Allpdb4v6i.ent.gz
pdb4v6i.ent (uncompressed file)
Header onlypdb4v6i.ent.gz
mmCIF format
mmCIF4v6i.cif.gz
XML format
All4v6i.xml.gz
No-atom4v6i-noatom.xml.gz
Ext-atom4v6i-extatom.xml.gz
Movie files
movie #1
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movie #2
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movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 3.3 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 3.3 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
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