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- PDB-5mmj: Structure of the small subunit of the chloroplast ribosome -

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Basic information

Entry
Database: PDB / ID: 5mmj
TitleStructure of the small subunit of the chloroplast ribosome
Descriptor50S ribosomal protein L31
Uncharacterized protein
Ribosome-binding factor PSRP1,chloroplastic/RNA Complex
(plastid ribosomal protein ...) x 2
(30S ribosomal protein ...) x 16
KeywordsRIBOSOME / chloroplast / translation / ribosome / cryo-EM
Specimen sourceSpinacia oleracea / plant / spinach / Spinach / ホウレンソウ
MethodElectron microscopy (3.6 Å resolution / Particle / Single particle)
AuthorsBieri, P. / Leibundgut, M. / Saurer, M. / Boehringer, D. / Ban, N.
CitationEMBO J., 2017, 36, 475-486

EMBO J., 2017, 36, 475-486 Yorodumi Papers
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Mar 1, 2017Structure modelDatabase references
1.2Aug 2, 2017Structure modelData collection / Derived calculationsem_software / pdbx_struct_conn_angle / struct_conn_em_software.name

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Assembly

Deposited unit
0: 50S ribosomal protein L31
8: plastid ribosomal protein bS1c
a: 16S ribosomal RNA
b: 30S ribosomal protein S2, chloroplastic
c: 30S ribosomal protein S3, chloroplastic
d: 30S ribosomal protein S4, chloroplastic
e: 30S ribosomal protein S5, chloroplastic
f: plastid ribosomal protein bS6c
g: 30S ribosomal protein S7, chloroplastic
h: 30S ribosomal protein S8, chloroplastic
i: plastid ribosomal protein uS9c
j: plastid ribosomal protein uS10c
k: 30S ribosomal protein S11, chloroplastic
l: 30S ribosomal protein S12, chloroplastic
m: plastid ribosomal protein uS13c
n: 30S ribosomal protein S14, chloroplastic
o: 30S ribosomal protein S15, chloroplastic
p: 30S ribosomal protein S16, chloroplastic
q: plastid ribosomal protein uS17c
r: 30S ribosomal protein S18, chloroplastic
s: 30S ribosomal protein S19 alpha, chloroplastic
t: plastid ribosomal protein bS20c
u: plastid ribosomal protein bS21c
v: 30S ribosomal protein 2, chloroplastic
w: 30S ribosomal protein 3, chloroplastic
x: 30S ribosomal protein S31, chloroplastic
y: Ribosome-binding factor PSRP1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)982,336212
Polyers977,83927
Non-polymers4,496185
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)127160
ΔGint (kcal/M)-2281
Surface area (Å2)312860
MethodPISA

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Components

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Polypeptide(L) , 2 types, 2 molecules 0y

#1: Polypeptide(L)50S ribosomal protein L31 / plastid ribosomal protein bL31c


Mass: 14748.201 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9R0R6

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)Ribosome-binding factor PSRP1, chloroplastic / plastid pY / 30S ribosomal protein 1 / CS-S5 / CS5 / Plastid-specific 30S ribosomal protein 1 / PSrp-1 / Ribosomal protein 1 / S22


Mass: 33799.266 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P19954

Cellular component

Molecular function

Biological process

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Plastid ribosomal protein ... , 8 types, 8 molecules 8fijmqtu

#2: Polypeptide(L)plastid ribosomal protein bS1c


Mass: 14826.253 Da / Num. of mol.: 1
Details: Residues were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea
#8: Polypeptide(L)plastid ribosomal protein bS6c


Mass: 23510.664 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9R0H2

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)plastid ribosomal protein uS9c


Mass: 22415.057 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RY17

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)plastid ribosomal protein uS10c


Mass: 21440.539 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RWE7

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)plastid ribosomal protein uS13c


Mass: 19310.641 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9R024

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)plastid ribosomal protein uS17c


Mass: 18151.936 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RRR0

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)plastid ribosomal protein bS20c


Mass: 20147.291 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea
#23: Polypeptide(L)plastid ribosomal protein bS21c


Mass: 20616.150 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RHF9

Cellular component

Molecular function

Biological process

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30S ribosomal protein ... , 16 types, 16 molecules bcdeghklno...

#4: Polypeptide(L)30S ribosomal protein S2, chloroplastic / plastid ribosomal protein uS2c


Mass: 26736.141 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P08242

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)30S ribosomal protein S3, chloroplastic / plastid ribosomal protein uS3c


Mass: 24965.156 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P09595

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S4, chloroplastic / plastid ribosomal protein uS4c


Mass: 23454.531 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P13788

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein S5, chloroplastic / plastid ribosomal protein uS5c


Mass: 33626.363 Da / Num. of mol.: 1
Details: Residues 122-150 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea / References: UniProt: Q9ST69

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein S7, chloroplastic / plastid ribosomal protein uS7c


Mass: 17378.309 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P82129

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)30S ribosomal protein S8, chloroplastic / plastid ribosomal protein uS8c


Mass: 15527.256 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P09597

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S11, chloroplastic / plastid ribosomal protein uS11c


Mass: 14927.551 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P06506

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S12, chloroplastic / plastid ribosomal protein uS12c


Mass: 13794.261 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P62128

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)30S ribosomal protein S14, chloroplastic / plastid ribosomal protein uS14c


Mass: 11809.832 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P06507

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein S15, chloroplastic / plastid ribosomal protein uS15c


Mass: 10778.763 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: Q9M3I4

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)30S ribosomal protein S16, chloroplastic / plastid ribosomal protein bS16c


Mass: 10454.237 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P28807

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S18, chloroplastic / plastid ribosomal protein uS18c


Mass: 12079.137 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: Q9M3K7

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)30S ribosomal protein S19 alpha, chloroplastic / plastid ribosomal protein uS19c / CS-S23


Mass: 10632.500 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P06508

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)30S ribosomal protein 2, chloroplastic / plastid ribosomal protein cS22 / Plastid-specific 30S ribosomal protein 2 / PSRP-2


Mass: 28327.863 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P82277

Cellular component

Molecular function

#25: Polypeptide(L)30S ribosomal protein 3, chloroplastic / plastid ribosomal protein cS23 / Plastid-specific 30S ribosomal protein 3 / PSRP-3


Mass: 20312.750 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P82412

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)30S ribosomal protein S31, chloroplastic / plastid ribosomal protein bTHXc / Plastid-specific 30S ribosomal protein 4 / PSRP-4


Mass: 10602.076 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P47910

Cellular component

Molecular function

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RNA chain / Non-polymers , 2 types, 186 molecules a

#28: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 185 / Formula: Mg
#3: RNA chain16S ribosomal RNA / plastid 16S rRNA


Mass: 483466.500 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: GenBank: 7636084

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Chloroplast 70S ribosome / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27
Source: NATURAL
Molecular weightValue: 2.4 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organelle: chloroplast / Organism: Spinacia oleracea / Tissue: leaf
Buffer solutionpH: 7.6
Buffer component
IDConc.UnitsNameFormulaBuffer ID
125mMTris hydrochlorideTris-HCl1
225mMPotassium chlorideKCl1
325mMMagnesium acetateMg(CH3COO)21
42mMDithiothreitolDTT1
50.05mMSpermine1
62mMSpermidine1
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of real images: 2796
Image scansMovie frames/image: 8 / Used frames/image: 2-8

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategoryDetailsImage processing IDImaging IDFitting ID
1EMAN1.9PARTICLE SELECTIONBatchboxer1
2EPUIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTIONCTF estimation1
5RELION1.4CTF CORRECTIONAmplitude correction1
8UCSF Chimera1.11.2MODEL FITTING1
10RELION1.4INITIAL EULER ASSIGNMENT1
11RELION1.4FINAL EULER ASSIGNMENT1
12RELION1.4CLASSIFICATION1
13RELION1.4RECONSTRUCTION1
14PHENIX1.11.1MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 326094
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 127031 / Symmetry type: POINT
Atomic model buildingOverall b value: 111.6 / Ref protocol: OTHER / Ref space: RECIPROCAL
Refine
Refine IDR factor R freeR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection R freeNumber reflection obsPercent reflection R freePercent reflection obsOverall SU MLSigma FOverall phase errorSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
10.24920.23540.23573.646300.2402936411687522.5199.930.551.0129.710.901.11MLHLFLAT BULK SOLVENT MODEL
ELECTRON MICROSCOPY
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00859305
ELECTRON MICROSCOPYf_angle_d1.08487437
ELECTRON MICROSCOPYf_dihedral_angle_d16.64626903
ELECTRON MICROSCOPYf_chiral_restr0.04410992
ELECTRON MICROSCOPYf_plane_restr0.0055572
Refine LS shell

Refine ID: ELECTRON MICROSCOPY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.64600.51380.49123.687599037843100.00
3.68750.42050.40913.7309102037921100.00
3.73090.41080.39403.776494337862100.00
3.77640.39730.38693.824298038564100.00
3.82420.38760.38113.874597038020100.00
3.87450.39400.36783.927697737784100.00
3.92760.37870.35263.983796437946100.00
3.98370.35800.34424.043298738004100.00
4.04320.34810.33494.106399538223100.00
4.10630.35450.32414.173796737663100.00
4.17370.32320.31224.2456100738382100.00
4.24560.33120.30094.322994837989100.00
4.32290.29770.28814.406098338005100.00
4.40600.29490.28284.496094437615100.00
4.49600.30030.27224.5937103338169100.00
4.59370.26810.26404.7006101138085100.00
4.70060.27080.25084.818299837811100.00
4.81820.24140.24014.9484101637918100.00
4.94840.24810.23365.094195838250100.00
5.09410.25470.22665.258595037875100.00
5.25850.22190.22125.4465101638114100.00
5.44650.20750.20695.664595538061100.00
5.66450.22650.20575.922494137771100.00
5.92240.20370.19336.2346101638109100.00
6.23460.20890.19486.625396338134100.00
6.62530.19250.17887.1369100637837100.00
7.13690.17400.16777.855197538057100.00
7.85510.18470.17228.991897837953100.00
8.99180.16760.156911.32899503772899.00
11.32890.15780.1490301.26309233769599.00

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