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Homology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.

by single particle reconstruction, at 9.4 A resolution

Movie

Orientation:

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1417, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1417, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4v61
TitleHomology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.
DescriptorRibosome
KeywordsRIBOSOME, SMALL RIBOSOMAL SUBUNIT, SPINACH CHLOROPLAST RIBOSOME, RIBONUCLEOPROTEIN PARTICLE, MACROMOLECULAR COMPLEX
AuthorsSharma, M.R., Wilson, D.N., Datta, P.P., Barat, C., Schluenzen, F., Fucini, P., Agrawal, R.K.
DateDeposition: 2007-11-09, Release: 2014-07-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1417, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1417, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1417

CiteFit

Cite: data citing same article

Fit: target map of fitting

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 104, Issue 49, Page 19315-20, Year 2007
TitleCryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
AuthorsManjuli R Sharma, Daniel N Wilson, Partha P Datta, Chandana Barat, Frank Schluenzen, Paola Fucini, Rajendra K Agrawal
Laboratory of Structural Pathology, Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsChloroplasts (chemistry), Cryoelectron Microscopy, Crystallography, X-Ray, Evolution, Molecular, Plant Proteins (chemistry), Plastids (chemistry), Protein Conformation, Ribosomal Proteins (chemistry), Ribosome Subunits, Large, Eukaryotic (chemistry), Ribosome Subunits, Small, Eukaryotic (chemistry), Spinacia oleracea (metabolism)
LinksDOI: 10.1073/pnas.0709856104, PubMed: 18042701, PMC: PMC2148287
Components
ID 1 : 16S rRNA
Image
Description16S rRNA
Typepolyribonucleotide
Formula weight483490.531 Da
Number of molecules1
ID1
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksGenBank: 7636084, Sequence view
ID 2 : Ribosomal Protein S2
Image
DescriptionRibosomal Protein S2
Typepolypeptide(L)
Formula weight26092.336 Da
Number of molecules1
ID2
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P08242, Sequence view
ID 3 : Ribosomal Protein S3
Image
DescriptionRibosomal Protein S3
Typepolypeptide(L)
Formula weight24965.156 Da
Number of molecules1
ID3
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P09595, Sequence view
ID 4 : Ribosomal Protein S4
Image
DescriptionRibosomal Protein S4
Typepolypeptide(L)
Formula weight23454.531 Da
Number of molecules1
ID4
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P13788, Sequence view
ID 5 : Ribosomal Protein S5
Image
DescriptionRibosomal Protein S5
Typepolypeptide(L)
Formula weight33626.363 Da
Number of molecules1
ID5
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9ST69, Sequence view
ID 6 : Ribosomal Protein S6
Image
DescriptionRibosomal Protein S6
Typepolypeptide(L)
Formula weight18870.361 Da
Number of molecules1
ID6
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82403, Sequence view
ID 7 : Ribosomal Protein S7
Image
DescriptionRibosomal Protein S7
Typepolypeptide(L)
Formula weight17378.309 Da
Number of molecules1
ID7
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82129, Sequence view
ID 8 : Ribosomal Protein S8
Image
DescriptionRibosomal Protein S8
Typepolypeptide(L)
Formula weight15527.256 Da
Number of molecules1
ID8
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P09597, Sequence view
ID 9 : Ribosomal Protein S9
Image
DescriptionRibosomal Protein S9
Typepolypeptide(L)
Formula weight21350.842 Da
Number of molecules1
ID9
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82278, Sequence view
ID 10 : Ribosomal Protein S10
Image
DescriptionRibosomal Protein S10
Typepolypeptide(L)
Formula weight21632.629 Da
Number of molecules1
ID10
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 11 : Ribosomal Protein S11
Image
DescriptionRibosomal Protein S11
Typepolypeptide(L)
Formula weight15085.706 Da
Number of molecules1
ID11
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P06506, Sequence view
ID 12 : Ribosomal Protein S12
Image
DescriptionRibosomal Protein S12
Typepolypeptide(L)
Formula weight13794.261 Da
Number of molecules1
ID12
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P62128, Sequence view
ID 13 : Ribosomal Protein S13
Image
DescriptionRibosomal Protein S13
Typepolypeptide(L)
Formula weight16306.087 Da
Number of molecules1
ID13
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82163, Sequence view
ID 14 : Ribosomal Protein S14
Image
DescriptionRibosomal Protein S14
Typepolypeptide(L)
Formula weight11809.832 Da
Number of molecules1
ID14
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P06507, Sequence view
ID 15 : Ribosomal Protein S15
Image
DescriptionRibosomal Protein S15
Typepolypeptide(L)
Formula weight10778.763 Da
Number of molecules1
ID15
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9M3I4, Sequence view
ID 16 : Ribosomal Protein S16
Image
DescriptionRibosomal Protein S16
Typepolypeptide(L)
Formula weight10454.237 Da
Number of molecules1
ID16
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P28807, Sequence view
ID 17 : Ribosomal Protein S17
Image
DescriptionRibosomal Protein S17
Typepolypeptide(L)
Formula weight15828.694 Da
Number of molecules1
ID17
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 18 : Ribosomal Protein S18
Image
DescriptionRibosomal Protein S18
Typepolypeptide(L)
Formula weight12337.430 Da
Number of molecules1
ID18
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9M3K7, Sequence view
ID 19 : Ribosomal Protein S19
Image
DescriptionRibosomal Protein S19
Typepolypeptide(L)
Formula weight10632.500 Da
Number of molecules1
ID19
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P06508, Sequence view
ID 20 : Ribosomal Protein S20
Image
DescriptionRibosomal Protein S20
Typepolypeptide(L)
Formula weight21866.373 Da
Number of molecules1
ID20
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 21 : Ribosomal Protein S21
Image
DescriptionRibosomal Protein S21
Typepolypeptide(L)
Formula weight21701.236 Da
Number of molecules1
ID21
Detailsmodeled using Escherichia coli 2AVY as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
Cellular location: chloroplast
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 22 : 23S rRNA
Image
Description23S rRNA
Typepolyribonucleotide
Formula weight911368.312 Da
Number of molecules1
ID22
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksGenBank: SOL400848, Sequence view
ID 23 : 5S rRNA
Image
Description5S rRNA
Typepolyribonucleotide
Formula weight37743.441 Da
Number of molecules1
ID23
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksGenBank: SOL400848, Sequence view
ID 24 : 4.8S rRNA
Image
Description4.8S rRNA
Typepolyribonucleotide
Formula weight33330.867 Da
Number of molecules1
ID24
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksGenBank: SOL400848, Sequence view
ID 25 : Ribosomal Protein L1
Image
DescriptionRibosomal Protein L1
Typepolypeptide(L)
Formula weight38681.484 Da
Number of molecules1
ID25
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9LE95, Sequence view
ID 26 : Ribosomal Protein L2
Image
DescriptionRibosomal Protein L2
Typepolypeptide(L)
Formula weight29480.168 Da
Number of molecules1
ID26
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P06509, Sequence view
ID 27 : Ribosomal Protein L3
Image
DescriptionRibosomal Protein L3
Typepolypeptide(L)
Formula weight28423.457 Da
Number of molecules1
ID27
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 28 : Ribosomal Protein L4
Image
DescriptionRibosomal Protein L4
Typepolypeptide(L)
Formula weight32479.617 Da
Number of molecules1
ID28
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: O49937, Sequence view
ID 29 : Ribosomal Protein L5
Image
DescriptionRibosomal Protein L5
Typepolypeptide(L)
Formula weight24248.189 Da
Number of molecules1
ID29
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82192, Sequence view
ID 30 : Ribosomal Protein L6
Image
DescriptionRibosomal Protein L6
Typepolypeptide(L)
Formula weight24747.686 Da
Number of molecules1
ID30
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 31 : Ribosomal Protein L9
Image
DescriptionRibosomal Protein L9
Typepolypeptide(L)
Formula weight22169.826 Da
Number of molecules1
ID31
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 32 : Ribosomal Protein L11
Image
DescriptionRibosomal Protein L11
Typepolypeptide(L)
Formula weight23689.980 Da
Number of molecules1
ID32
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P31164, Sequence view
ID 33 : Ribosomal Protein L13
Image
DescriptionRibosomal Protein L13
Typepolypeptide(L)
Formula weight28211.629 Da
Number of molecules1
ID33
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P12629, Sequence view
ID 34 : Ribosomal Protein L14
Image
DescriptionRibosomal Protein L14
Typepolypeptide(L)
Formula weight13484.741 Da
Number of molecules1
ID34
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P09596, Sequence view
ID 35 : Ribosomal Protein L15
Image
DescriptionRibosomal Protein L15
Typepolypeptide(L)
Formula weight27491.221 Da
Number of molecules1
ID35
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 36 : Ribosomal Protein L16
Image
DescriptionRibosomal Protein L16
Typepolypeptide(L)
Formula weight15328.068 Da
Number of molecules1
ID36
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P17353, Sequence view
ID 37 : Ribosomal Protein L17
Image
DescriptionRibosomal Protein L17
Typepolypeptide(L)
Formula weight22983.852 Da
Number of molecules1
ID37
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 38 : Ribosomal Protein L18
Image
DescriptionRibosomal Protein L18
Typepolypeptide(L)
Formula weight17850.727 Da
Number of molecules1
ID38
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 39 : Ribosomal Protein L19
Image
DescriptionRibosomal Protein L19
Typepolypeptide(L)
Formula weight26121.254 Da
Number of molecules1
ID39
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82413, Sequence view
ID 40 : Ribosomal Protein L20
Image
DescriptionRibosomal Protein L20
Typepolypeptide(L)
Formula weight14617.331 Da
Number of molecules1
ID40
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P28803, Sequence view
ID 41 : Ribosomal Protein L21
Image
DescriptionRibosomal Protein L21
Typepolypeptide(L)
Formula weight28554.883 Da
Number of molecules1
ID41
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P24613, Sequence view
ID 42 : Ribosomal Protein L22
Image
DescriptionRibosomal Protein L22
Typepolypeptide(L)
Formula weight23276.654 Da
Number of molecules1
ID42
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P09594, Sequence view
ID 43 : Ribosomal Protein L23
Image
DescriptionRibosomal Protein L23
Typepolypeptide(L)
Formula weight21832.164 Da
Number of molecules1
ID43
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: Q9LWB5, Sequence view
ID 44 : Ribosomal Protein L24
Image
DescriptionRibosomal Protein L24
Typepolypeptide(L)
Formula weight21481.088 Da
Number of molecules1
ID44
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P27683, Sequence view
ID 45 : Ribosomal Protein L27
Image
DescriptionRibosomal Protein L27
Typepolypeptide(L)
Formula weight21771.951 Da
Number of molecules1
ID45
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 46 : Ribosomal Protein L28
Image
DescriptionRibosomal Protein L28
Typepolypeptide(L)
Formula weight16730.691 Da
Number of molecules1
ID46
Detailsmodeled using Thermus thermophilus 2J01 as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 47 : Ribosomal Protein L29
Image
DescriptionRibosomal Protein L29
Typepolypeptide(L)
Formula weight19415.543 Da
Number of molecules1
ID47
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 48 : Ribosomal Protein L31
Image
DescriptionRibosomal Protein L31
Typepolypeptide(L)
Formula weight16060.906 Da
Number of molecules1
ID48
Detailsmodeled using Thermus thermophilus 2J01 as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
ID 49 : Ribosomal Protein L32
Image
DescriptionRibosomal Protein L32
Typepolypeptide(L)
Formula weight6650.969 Da
Number of molecules1
ID49
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P28804, Sequence view
ID 50 : Ribosomal Protein L33
Image
DescriptionRibosomal Protein L33
Typepolypeptide(L)
Formula weight7668.121 Da
Number of molecules1
ID50
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P28805, Sequence view
ID 51 : Ribosomal Protein L34
Image
DescriptionRibosomal Protein L34
Typepolypeptide(L)
Formula weight16126.633 Da
Number of molecules1
ID51
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P82244, Sequence view
ID 52 : Ribosomal Protein L35
Image
DescriptionRibosomal Protein L35
Typepolypeptide(L)
Formula weight17376.322 Da
Number of molecules1
ID52
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksUniProt: P23326, Sequence view
ID 53 : Ribosomal Protein L36
Image
DescriptionRibosomal Protein L36
Typepolypeptide(L)
Formula weight11509.490 Da
Number of molecules1
ID53
Detailsmodeled using Escherichia coli 2AWB as template
SourceMethod: Isolated from a natural source
Src id: 1
Common name: spinach
NCBI taxonomy: ID:3562
Organism scientific: Spinacea oleracea
LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
Detailstight couple chloroplast 70S ribosomes
Namespinach 70S chloro-ribosome
Buffer
Name10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.6
Vitrification
Details5 microliters applied to the grid then blotted for 3 seconds with Whatman number 1 filter paper before plunging in liquid ethane.
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: Phillips Tecnai F20 FEG
Electron gun
Electron sourceFEG
Accelerating voltage200 kV
Electron dose2000 e/A**2
Illumination modeFlood Beam
Lens
ModeBright Field
MagnificationCalibrated: 50760 X, Nominal: 50000 X
CsNominal: 2 mm
Nominal defocusMax: 3500 nm, Min: 700 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature93 Kelvin
Detector
TypeKodak S0163 Film
Processing
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size2.76 A/pix
CTF correction methodCTF correction for each Micrograph
DetailsAn 11.5 A E.coli 70S ribosome map was used as initial reference and then resulting 18 A map from reconstruction of 70S chloro-ribosome was used as a reference for iterative refinement
Magnification calibration50,760
MethodThe projection matching procedure within the SPIDER software was used to get 3D map
Resolution9.4 A
3D fitting
MethodCross-Correlation based manual fitting in 'O'
Refinement ProtocolRigid Body
Refinement SpaceREAL
Target criteriaBest visual fit using the program O
3D fitting list
3D Fitting ID1
PDB entry ID2XYZ and 2ZXY for small and large subunit respectively
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms51118
Nucleic acid atoms31745
Protein atoms19373
Download
PDB format
Allpdb4v61.ent.gz
pdb4v61.ent (uncompressed file)
Header onlypdb4v61.ent.gz
mmCIF format
mmCIF4v61.cif.gz
XML format
All4v61.xml.gz
No-atom4v61-noatom.xml.gz
Ext-atom4v61-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 3.9 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 3.2 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB