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- PDB-4v61: Homology model for the Spinach chloroplast 30S subunit fitted to ... -

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Basic information

Entry
Database: PDB / ID: 4v61
TitleHomology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.
Components
  • (Ribosomal Protein ...) x 49
  • 16S rRNA
  • 23S rRNA
  • 4.8S rRNA
  • 5S rRNA
KeywordsRIBOSOME / SMALL RIBOSOMAL SUBUNIT / SPINACH CHLOROPLAST RIBOSOME / RIBONUCLEOPROTEIN PARTICLE / MACROMOLECULAR COMPLEX
Function / homology
Function and homology information


plastid small ribosomal subunit / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...plastid small ribosomal subunit / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S14, bacterial/plastid ...Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L20 / Ribosomal protein S12, bacterial-type / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Translation elongation factor EF1B/ribosomal protein S6 / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / 50S ribosomal protein uL4 / Ribosomal protein S2 signature 2. / Ribosomal protein L13, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein L2 signature. / Ribosomal protein S2 signature 1. / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c / Large ribosomal subunit protein uL2cz/uL2cy / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein uL22c / Small ribosomal subunit protein uS3c / Large ribosomal subunit protein uL14c / Small ribosomal subunit protein uS8c / Large ribosomal subunit protein uL13c / Small ribosomal subunit protein uS4c / Large ribosomal subunit protein uL16c / Large ribosomal subunit protein bL35c / Large ribosomal subunit protein bL21c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein bL20c / Large ribosomal subunit protein bL32c / Large ribosomal subunit protein bL33c / Small ribosomal subunit protein bS16c / Large ribosomal subunit protein uL11c / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein uS7cz/uS7cy / Small ribosomal subunit protein uS13c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein bL34c / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL1c / Large ribosomal subunit protein uL23c / Small ribosomal subunit protein uS15c / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS5c
Similarity search - Component
Biological speciesSpinacea oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsSharma, M.R. / Wilson, D.N. / Datta, P.P. / Barat, C. / Schluenzen, F. / Fucini, P. / Agrawal, R.K.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2007
Title: Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
Authors: Manjuli R Sharma / Daniel N Wilson / Partha P Datta / Chandana Barat / Frank Schluenzen / Paola Fucini / Rajendra K Agrawal /
Abstract: Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally ...Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (PSRPs); however, it is unclear to what extent these proteins play structural or regulatory roles during translation. We have obtained a three-dimensional cryo-EM map of the spinach 70S chloro-ribosome, revealing the overall structural organization to be similar to bacterial ribosomes. Fitting of the conserved portions of the x-ray crystallographic structure of the bacterial 70S ribosome into our cryo-EM map of the chloro-ribosome reveals the positions of PRP extensions and the locations of the PSRPs. Surprisingly, PSRP1 binds in the decoding region of the small (30S) ribosomal subunit, in a manner that would preclude the binding of messenger and transfer RNAs to the ribosome, suggesting that PSRP1 is a translation factor rather than a ribosomal protein. PSRP2 and PSRP3 appear to structurally compensate for missing segments of the 16S rRNA within the 30S subunit, whereas PSRP4 occupies a position buried within the head of the 30S subunit. One of the two PSRPs in the large (50S) ribosomal subunit lies near the tRNA exit site. Furthermore, we find a mass of density corresponding to chloro-ribosome recycling factor; domain II of this factor appears to interact with the flexible C-terminal domain of PSRP1. Our study provides evolutionary insights into the structural and functional roles that the PSRPs play during protein synthesis in chloroplasts.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3BBO, 3BBN
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Other
Category: atom_sites / em_image_scans ...atom_sites / em_image_scans / struct_ref_seq / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
AA: 16S rRNA
AB: Ribosomal Protein S2
AC: Ribosomal Protein S3
AD: Ribosomal Protein S4
AE: Ribosomal Protein S5
AF: Ribosomal Protein S6
AG: Ribosomal Protein S7
AH: Ribosomal Protein S8
AI: Ribosomal Protein S9
AJ: Ribosomal Protein S10
AK: Ribosomal Protein S11
AL: Ribosomal Protein S12
AM: Ribosomal Protein S13
AN: Ribosomal Protein S14
AO: Ribosomal Protein S15
AP: Ribosomal Protein S16
AQ: Ribosomal Protein S17
AR: Ribosomal Protein S18
AS: Ribosomal Protein S19
AT: Ribosomal Protein S20
AU: Ribosomal Protein S21
BA: 23S rRNA
BB: 5S rRNA
BC: 4.8S rRNA
BD: Ribosomal Protein L1
BE: Ribosomal Protein L2
BF: Ribosomal Protein L3
BG: Ribosomal Protein L4
BH: Ribosomal Protein L5
BI: Ribosomal Protein L6
BJ: Ribosomal Protein L9
BK: Ribosomal Protein L11
BL: Ribosomal Protein L13
BM: Ribosomal Protein L14
BN: Ribosomal Protein L15
BO: Ribosomal Protein L16
BP: Ribosomal Protein L17
BQ: Ribosomal Protein L18
BR: Ribosomal Protein L19
BS: Ribosomal Protein L20
BT: Ribosomal Protein L21
BU: Ribosomal Protein L22
BV: Ribosomal Protein L23
BW: Ribosomal Protein L24
BX: Ribosomal Protein L27
BY: Ribosomal Protein L28
BZ: Ribosomal Protein L29
B1: Ribosomal Protein L31
B2: Ribosomal Protein L32
B3: Ribosomal Protein L33
B4: Ribosomal Protein L34
B5: Ribosomal Protein L35
B6: Ribosomal Protein L36


Theoretical massNumber of molelcules
Total (without water)2,447,89153
Polymers2,447,89153
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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RNA chain , 4 types, 4 molecules AABABBBC

#1: RNA chain 16S rRNA


Mass: 483490.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: GenBank: 7636084
#22: RNA chain 23S rRNA


Mass: 911368.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: EMBL: SOL400848
#23: RNA chain 5S rRNA


Mass: 37743.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: EMBL: SOL400848
#24: RNA chain 4.8S rRNA


Mass: 33330.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: EMBL: SOL400848

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Ribosomal Protein ... , 49 types, 49 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUBDBEBFBGBHBIBJBKBLBM...

#2: Protein Ribosomal Protein S2


Mass: 26092.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P08242
#3: Protein Ribosomal Protein S3


Mass: 24965.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P09595
#4: Protein Ribosomal Protein S4


Mass: 23454.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P13788
#5: Protein Ribosomal Protein S5


Mass: 33626.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: Q9ST69
#6: Protein Ribosomal Protein S6


Mass: 18870.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82403
#7: Protein Ribosomal Protein S7


Mass: 17378.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82129
#8: Protein Ribosomal Protein S8


Mass: 15527.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P09597
#9: Protein Ribosomal Protein S9


Mass: 21350.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82278
#10: Protein Ribosomal Protein S10


Mass: 21632.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#11: Protein Ribosomal Protein S11


Mass: 15085.706 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P06506
#12: Protein Ribosomal Protein S12


Mass: 13794.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P62128
#13: Protein Ribosomal Protein S13


Mass: 16306.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82163
#14: Protein Ribosomal Protein S14


Mass: 11809.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P06507
#15: Protein Ribosomal Protein S15


Mass: 10778.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: Q9M3I4
#16: Protein Ribosomal Protein S16


Mass: 10454.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P28807
#17: Protein Ribosomal Protein S17


Mass: 15828.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#18: Protein Ribosomal Protein S18


Mass: 12337.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: Q9M3K7
#19: Protein Ribosomal Protein S19


Mass: 10632.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P06508
#20: Protein Ribosomal Protein S20


Mass: 21866.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#21: Protein Ribosomal Protein S21


Mass: 21701.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#25: Protein Ribosomal Protein L1


Mass: 38681.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: Q9LE95
#26: Protein Ribosomal Protein L2


Mass: 29480.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P06509
#27: Protein Ribosomal Protein L3


Mass: 28423.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#28: Protein Ribosomal Protein L4


Mass: 32479.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: O49937
#29: Protein Ribosomal Protein L5


Mass: 24248.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P82192
#30: Protein Ribosomal Protein L6


Mass: 24747.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#31: Protein Ribosomal Protein L9


Mass: 22169.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#32: Protein Ribosomal Protein L11


Mass: 23689.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P31164
#33: Protein Ribosomal Protein L13


Mass: 28211.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P12629
#34: Protein Ribosomal Protein L14


Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P09596
#35: Protein Ribosomal Protein L15


Mass: 27491.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#36: Protein Ribosomal Protein L16


Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P17353
#37: Protein Ribosomal Protein L17


Mass: 22983.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#38: Protein Ribosomal Protein L18


Mass: 17850.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#39: Protein Ribosomal Protein L19


Mass: 26121.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P82413
#40: Protein Ribosomal Protein L20


Mass: 14617.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P28803
#41: Protein Ribosomal Protein L21


Mass: 28554.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P24613
#42: Protein Ribosomal Protein L22


Mass: 23276.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P09594
#43: Protein Ribosomal Protein L23


Mass: 21832.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: Q9LWB5
#44: Protein Ribosomal Protein L24


Mass: 21481.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P27683
#45: Protein Ribosomal Protein L27


Mass: 21771.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#46: Protein Ribosomal Protein L28


Mass: 16730.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: modeled using Thermus thermophilus 2J01 as template
Source: (natural) Spinacea oleracea (spinach)
#47: Protein Ribosomal Protein L29


Mass: 19415.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#48: Protein Ribosomal Protein L31


Mass: 16060.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: modeled using Thermus thermophilus 2J01 as template
Source: (natural) Spinacea oleracea (spinach)
#49: Protein Ribosomal Protein L32


Mass: 6650.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P28804
#50: Protein Ribosomal Protein L33


Mass: 7668.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P28805
#51: Protein Ribosomal Protein L34


Mass: 16126.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P82244
#52: Protein Ribosomal Protein L35


Mass: 17376.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P23326
#53: Protein Ribosomal Protein L36


Mass: 11509.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: spinach 70S chloro-ribosome / Type: RIBOSOME / Details: tight couple chloroplast 70S ribosomes
Buffer solutionName: 10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME / pH: 7.6
Details: 10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: 5 microliters applied to the grid then blotted for 3 seconds with Whatman number 1 filter paper before plunging in liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50760 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: CTF correction for each Micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: The projection matching procedure within the SPIDER software was used to get 3D map
Resolution: 9.4 Å / Num. of particles: 86370 / Actual pixel size: 2.76 Å / Magnification calibration: 50,760
Details: An 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
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Best visual fit using the program O
Details: METHOD--Cross-Correlation based manual fitting in O REFINEMENT PROTOCOL--Rigid Body
Atomic model building

3D fitting-ID: 1 / Details: 2XYZ AND 2ZXY FOR SMALL AND LARGE SUBUNIT RESPECTIVELY / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
12XYZ

2xyz

2XYZ1
22ZXY

2zxy

2ZXY2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms19373 31745 0 0 51118

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