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- PDB-5x8r: Structure of the 30S small subunit of chloroplast ribosome from s... -

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Basic information

Entry
Database: PDB / ID: 5x8r
TitleStructure of the 30S small subunit of chloroplast ribosome from spinach
Components
  • (30S ribosomal protein ...) x 17
  • 16S rRNA
  • protein S10
  • protein S17
  • protein S20
  • protein S21
  • protein bTHXc
  • protein cS22
  • protein cS23
  • protein plastid pY
KeywordsRIBOSOME / Cryo-EM / chloroplast ribosome
Function / homology
Function and homology information


plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / ribosomal small subunit binding / chloroplast / ribosomal small subunit biogenesis ...plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / ribosomal small subunit binding / chloroplast / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Helix Hairpins - #1480 / Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus ...Helix Hairpins - #1480 / Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein S1-like / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein / S1 domain profile. / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / RNA-binding domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome-binding factor PSRP1, chloroplastic / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein cS23 / Small ribosomal subunit protein bTHXc ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome-binding factor PSRP1, chloroplastic / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein cS23 / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Uncharacterized protein / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c / Small ribosomal subunit protein uS2c / Small ribosomal subunit protein uS3c / Small ribosomal subunit protein uS8c / Small ribosomal subunit protein uS4c / Ribosome-binding factor PSRP1, chloroplastic / Small ribosomal subunit protein bS16c / Small ribosomal subunit protein bS1c / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS7cz/uS7cy / 30S ribosomal protein S20, chloroplastic / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS13c / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS6c alpha / Small ribosomal subunit protein cS23 / Small ribosomal subunit protein uS15c / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS5c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAhmed, T. / Shi, J. / Bhushan, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
MOEAcRF Tier 1, 2014-T1-001-019 (RG32/14) Singapore
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Authors: Tofayel Ahmed / Jian Shi / Shashi Bhushan /
Abstract: Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, ...Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.
History
DepositionMar 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jun 6, 2018Group: Data collection / Category: em_image_scans / em_software
Item: _em_image_scans.dimension_height / _em_image_scans.dimension_width / _em_software.name
Revision 1.4Oct 16, 2019Group: Data collection / Other / Category: atom_sites / cell
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] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.5Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
b: 30S ribosomal protein S2, chloroplastic
c: 30S ribosomal protein S3, chloroplastic
e: 30S ribosomal protein S5, chloroplastic
f: 30S ribosomal protein S6 alpha, chloroplastic
g: 30S ribosomal protein S7, chloroplastic
h: 30S ribosomal protein S8, chloroplastic
i: 30S ribosomal protein S9, chloroplastic
j: protein S10
k: 30S ribosomal protein S11, chloroplastic
l: 30S ribosomal protein S12, chloroplastic
m: 30S ribosomal protein S13, chloroplastic
o: 30S ribosomal protein S15, chloroplastic
p: 30S ribosomal protein S16, chloroplastic
q: protein S17
r: 30S ribosomal protein S18, chloroplastic
s: 30S ribosomal protein S19 alpha, chloroplastic
t: protein S20
u: protein S21
y: protein plastid pY
a: 16S rRNA
w: protein cS23
d: 30S ribosomal protein S4, chloroplastic
v: protein cS22
n: 30S ribosomal protein S14, chloroplastic
x: protein bTHXc
8: 30S ribosomal protein S1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)913,91826
Polymers913,91826
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area101650 Å2
ΔGint-770 kcal/mol
Surface area316430 Å2

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Components

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30S ribosomal protein ... , 17 types, 17 molecules bcefghiklmoprsdn8

#1: Protein 30S ribosomal protein S2, chloroplastic / Ribosome


Mass: 26736.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P08242
#2: Protein 30S ribosomal protein S3, chloroplastic / Ribosome


Mass: 24965.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09595
#3: Protein 30S ribosomal protein S5, chloroplastic / Ribosome


Mass: 27696.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9ST69
#4: Protein 30S ribosomal protein S6 alpha, chloroplastic / Ribosome


Mass: 16341.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82403
#5: Protein 30S ribosomal protein S7, chloroplastic / Ribosome


Mass: 17378.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82129
#6: Protein 30S ribosomal protein S8, chloroplastic / Ribosome


Mass: 15527.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09597
#7: Protein 30S ribosomal protein S9, chloroplastic / Ribosome


Mass: 17092.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82278
#9: Protein 30S ribosomal protein S11, chloroplastic / Ribosome


Mass: 14927.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06506
#10: Protein 30S ribosomal protein S12, chloroplastic / Ribosome


Mass: 13794.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62128
#11: Protein 30S ribosomal protein S13, chloroplastic / Ribosome


Mass: 14418.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82163, UniProt: B8AQA7*PLUS
#12: Protein 30S ribosomal protein S15, chloroplastic / Ribosome


Mass: 10778.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3I4
#13: Protein 30S ribosomal protein S16, chloroplastic / Ribosome


Mass: 10454.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28807
#15: Protein 30S ribosomal protein S18, chloroplastic / Ribosome


Mass: 12079.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3K7
#16: Protein 30S ribosomal protein S19 alpha, chloroplastic / Ribosome / CS-S23


Mass: 10632.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06508
#22: Protein 30S ribosomal protein S4, chloroplastic / Ribosome


Mass: 23454.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P13788
#24: Protein 30S ribosomal protein S14, chloroplastic / Ribosome


Mass: 11809.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06507
#26: Protein 30S ribosomal protein S1, chloroplastic / Ribosome / CS1


Mass: 40472.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P29344

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Protein , 7 types, 7 molecules jqtuywv

#8: Protein protein S10


Mass: 13882.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RWE7, UniProt: P82162*PLUS
#14: Protein protein S17


Mass: 12195.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RRR0, UniProt: P82137*PLUS
#17: Protein protein S20


Mass: 12178.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82130*PLUS
#18: Protein protein S21


Mass: 16096.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RHF9, UniProt: P82024*PLUS
#19: Protein protein plastid pY


Mass: 26851.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHQ6, UniProt: P19954*PLUS
#21: Protein protein cS23


Mass: 13808.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RJX3, UniProt: P82412*PLUS
#23: Protein protein cS22


Mass: 21691.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R1W7, UniProt: P82277*PLUS

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RNA chain / Protein/peptide , 2 types, 2 molecules ax

#20: RNA chain 16S rRNA /


Mass: 483466.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084
#25: Protein/peptide protein bTHXc


Mass: 5188.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RMU8, UniProt: P47910*PLUS

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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: 30S small subunit of chloroplast ribosome from spinach
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 7.6
Details: 20 mM Tris HCl, pH 7.6, 100 mM KCl, 10 mM MgOAc, 100 mM sucrose, 7 mM 2-mercaptoethanol, 1 unit/ml RNase inhibitor, 0.1% protease inhibitor
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 133333 X / Nominal defocus max: 3700 nm / Nominal defocus min: 400 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3700 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3161
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 25 / Used frames/image: 1-25

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Processing

EM software
IDNameCategory
1EMAN2particle selection
4CTFFIND3CTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 187946
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81305 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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