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- PDB-5h1s: Structure of the large subunit of the chloro-ribosome -

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Basic information

Entry
Database: PDB / ID: 5h1s
TitleStructure of the large subunit of the chloro-ribosome
Components
  • (50S ribosomal protein ...) x 29
  • 23S rRNA
  • 5S rRNA
  • Spinach chloroplast 4.5S rRNA
KeywordsRIBOSOME / Cryo-EM / chloro-ribosome
Function / homology
Function and homology information


plastid translation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast thylakoid membrane / chloroplast / DNA-templated transcription termination / large ribosomal subunit / transferase activity / 5S rRNA binding ...plastid translation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast thylakoid membrane / chloroplast / DNA-templated transcription termination / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; ...Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / RRM (RNA recognition motif) domain / Single Sheet / Nucleic acid-binding proteins / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein uL2cz/uL2cy / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein uL14c / Large ribosomal subunit protein bL36c / Large ribosomal subunit protein uL13c / Large ribosomal subunit protein uL16c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein bL35c / Large ribosomal subunit protein bL21c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein bL20c / Large ribosomal subunit protein bL32c / Large ribosomal subunit protein bL33c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL34c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL23c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAhmed, T. / Yin, Z. / Bhushan, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
MOEAcRF Tier 1, 2014-T1-001-019 (RG32/14) Singapore
CitationJournal: Sci Rep / Year: 2016
Title: Cryo-EM structure of the large subunit of the spinach chloroplast ribosome.
Authors: Tofayel Ahmed / Zhan Yin / Shashi Bhushan /
Abstract: Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ...Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features.
History
DepositionOct 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
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Revision 1.1Feb 8, 2017Group: Refinement description
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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
C: Spinach chloroplast 4.5S rRNA
B: 5S rRNA
L: 50S ribosomal protein L13, chloroplastic
M: 50S ribosomal protein L14, chloroplastic
N: 50S ribosomal protein L15
O: 50S ribosomal protein L16, chloroplastic
P: 50S ribosomal protein L17
Q: 50S ribosomal protein L18
R: 50S ribosomal protein L19, chloroplastic
S: 50S ribosomal protein L20, chloroplastic
T: 50S ribosomal protein L21, chloroplastic
U: 50S ribosomal protein L22, chloroplastic
V: 50S ribosomal protein L23, chloroplastic
W: 50S ribosomal protein L24, chloroplastic
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
E: 50S ribosomal protein L2, chloroplastic
b: 50S ribosomal protein L32, chloroplastic
c: 50S ribosomal protein L33, chloroplastic
d: 50S ribosomal protein L34, chloroplastic
e: 50S ribosomal protein L35, chloroplastic
f: 50S ribosomal protein L36, chloroplastic
F: 50S ribosomal protein L3
G: 50S ribosomal protein L4, chloroplastic
H: 50S ribosomal protein L5, chloroplastic
I: 50S ribosomal protein L6
J: 50S ribosomal protein L9
g: 50S ribosomal protein 5 alpha, chloroplastic
a: 50S ribosomal protein L31
h: 50S ribosomal protein 6, chloroplastic


Theoretical massNumber of molelcules
Total (without water)1,445,31132
Polymers1,445,31132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area168100 Å2
ΔGint-1481 kcal/mol
Surface area502590 Å2

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Components

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RNA chain , 3 types, 3 molecules ACB

#1: RNA chain 23S rRNA


Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: AJ400848
#2: RNA chain Spinach chloroplast 4.5S rRNA / 4.8S rRNA


Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 175996
#3: RNA chain 5S rRNA


Mass: 39014.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)

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50S ribosomal protein ... , 29 types, 29 molecules LMNOPQRSTUVWXYZEbcdefFGHIJgah

#4: Protein 50S ribosomal protein L13, chloroplastic / CL13


Mass: 22123.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629
#5: Protein 50S ribosomal protein L14, chloroplastic / Ribosomal protein CS-L29


Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09596
#6: Protein 50S ribosomal protein L15 / L15


Mass: 20680.062 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-271 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHT0, UniProt: P22798*PLUS
#7: Protein 50S ribosomal protein L16, chloroplastic / Ribosomal protein CS-L24


Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17353
#8: Protein 50S ribosomal protein L17 / L17


Mass: 13466.902 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 11-126 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RLJ4, UniProt: P82194*PLUS
#9: Protein 50S ribosomal protein L18 / L18


Mass: 13801.939 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 44-166 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QQ60, UniProt: P82195*PLUS
#10: Protein 50S ribosomal protein L19, chloroplastic / CL19


Mass: 17597.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413
#11: Protein 50S ribosomal protein L20, chloroplastic


Mass: 15594.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803
#12: Protein 50S ribosomal protein L21, chloroplastic / CL21 / CS-L7


Mass: 22793.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#13: Protein 50S ribosomal protein L22, chloroplastic / Ribosomal protein CS-L13


Mass: 23292.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09594
#14: Protein 50S ribosomal protein L23, chloroplastic / PRPL23


Mass: 13575.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5
#15: Protein 50S ribosomal protein L24, chloroplastic / CL24


Mass: 16552.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27683
#16: Protein 50S ribosomal protein L27


Mass: 15326.538 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 58-194 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4I2, UniProt: P82190*PLUS
#17: Protein 50S ribosomal protein L28 / L28


Mass: 9016.668 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-148 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RD02, UniProt: P82245*PLUS
#18: Protein 50S ribosomal protein L29 / L29


Mass: 12903.116 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 60-168 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R7W8, UniProt: P82248*PLUS
#19: Protein 50S ribosomal protein L2, chloroplastic / Ribosomal protein CS-L4


Mass: 29722.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509
#20: Protein 50S ribosomal protein L32, chloroplastic


Mass: 6519.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804
#21: Protein 50S ribosomal protein L33, chloroplastic


Mass: 7536.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#22: Protein 50S ribosomal protein L34, chloroplastic / CL34


Mass: 6692.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244
#23: Protein 50S ribosomal protein L35, chloroplastic / CL35


Mass: 8459.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326
#24: Protein/peptide 50S ribosomal protein L36, chloroplastic


Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230
#25: Protein 50S ribosomal protein L3 / L3


Mass: 24117.328 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 85-305 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QEC7, UniProt: P82191*PLUS
#26: Protein 50S ribosomal protein L4, chloroplastic / R-protein L4


Mass: 27202.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: O49937
#27: Protein 50S ribosomal protein L5, chloroplastic


Mass: 24248.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82192
#28: Protein 50S ribosomal protein L6 / L6


Mass: 20263.604 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-220 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4N9, UniProt: P82193*PLUS
#29: Protein 50S ribosomal protein L9


Mass: 17669.951 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-196 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RQ91, UniProt: P82180*PLUS
#30: Protein 50S ribosomal protein 5 alpha, chloroplastic / 50S ribosomal protein L40 / CL40 / Plastid-specific 50S ribosomal protein 5 alpha / PSRP-5


Mass: 15351.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27684
#31: Protein 50S ribosomal protein L31


Mass: 10801.521 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 37-130 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0R6, UniProt: P82249*PLUS
#32: Protein 50S ribosomal protein 6, chloroplastic / CL25 / Plastid-specific 50S ribosomal protein 6 / PSRP-6


Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82411

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Details

Has protein modificationY

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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: Chloro-ribosome 50S / 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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 78000 X / Calibrated magnification: 109375 X / Nominal defocus max: 2500 nm / Nominal defocus min: 200 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2500 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: 26 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1590
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

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Processing

SoftwareName: PHENIX / Version: dev_2210: / Classification: refinement
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: 338305
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174949 / Algorithm: FOURIER SPACE / Num. of class averages: 20 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01398895
ELECTRON MICROSCOPYf_angle_d1.234148525
ELECTRON MICROSCOPYf_dihedral_angle_d20.89358950
ELECTRON MICROSCOPYf_chiral_restr0.0618988
ELECTRON MICROSCOPYf_plane_restr0.0538212

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