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- PDB-5mmi: Structure of the large subunit of the chloroplast ribosome -

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Entry
Database: PDB / ID: 5mmi
TitleStructure of the large subunit of the chloroplast ribosome
DescriptorUncharacterized protein
(50S ribosomal protein ...) x 17
KeywordsRIBOSOME / chloroplast / translation / ribosome / cryo-EM
Specimen sourceSpinacia oleracea / plant / spinach / Spinach / ホウレンソウ
MethodElectron microscopy (3.2 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
1: 50S ribosomal protein L32, chloroplastic
2: 50S ribosomal protein L33, chloroplastic
3: 50S ribosomal protein L34, chloroplastic
4: 50S ribosomal protein L35, chloroplastic
5: 50S ribosomal protein L36, chloroplastic
6: plastid ribosomal protein cL37, PSRP5
7: 50S ribosomal protein 6, chloroplastic
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2, chloroplastic
D: plastid ribosomal protein uL3c
E: plastid ribosomal protein uL4c
F: plastid ribosomal protein uL5c
G: plastid ribosomal protein uL6c
H: plastid ribosomal protein bL9c
I: plastid ribosomal protein uL10c
J: 50S ribosomal protein L11, chloroplastic
K: 50S ribosomal protein L13, chloroplastic
L: 50S ribosomal protein L14, chloroplastic
M: plastid ribosomal protein uL15c
N: 50S ribosomal protein L16, chloroplastic
O: plastid ribosomal protein bL17c
P: plastid ribosomal protein uL18c
Q: 50S ribosomal protein L19, chloroplastic
R: 50S ribosomal protein L20, chloroplastic
S: 50S ribosomal protein L21, chloroplastic
T: 50S ribosomal protein L22, chloroplastic
U: 50S ribosomal protein L23, chloroplastic
V: plastid ribosomal protein uL24c
W: 4.5S ribosomal RNA
X: plastid ribosomal protein bL27c
Y: plastid ribosomal protein bL28c
Z: plastid ribosomal protein uL29c
z: E-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,625,172538
Polyers1,612,86435
Non-polymers12,308503
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)9140
ΔGint (kcal/M)-101
Surface area (Å2)31260
MethodPISA

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Components

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50S ribosomal protein ... , 17 types, 17 molecules 0123457CJK...

#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

#2: Polypeptide(L)50S ribosomal protein L32, chloroplastic / plastid ribosomal protein bL32c


Mass: 6650.969 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P28804

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)50S ribosomal protein L33, chloroplastic / plastid ribosomal protein bL33c


Mass: 7668.121 Da / Num. of mol.: 1 / Details: Zn-binding protein / Source: (natural) Spinacia oleracea / References: UniProt: P28805

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)50S ribosomal protein L34, chloroplastic / plastid ribosomal protein bL34c / CL34


Mass: 16126.633 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P82244

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)50S ribosomal protein L35, chloroplastic / plastid ribosomal protein bL35c / CL35


Mass: 17376.322 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P23326

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)50S ribosomal protein L36, chloroplastic / plastid ribosomal protein bL36c


Mass: 4414.462 Da / Num. of mol.: 1 / Details: Zn-binding protein / Source: (natural) Spinacia oleracea / References: UniProt: P12230

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)50S ribosomal protein 6, chloroplastic / plastid ribosomal protein cL38 / PSRP6 / CL25 / Plastid-specific 50S ribosomal protein 6 / PSRP-6


Mass: 12080.688 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P82411

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)50S ribosomal protein L2, chloroplastic / plastid ribosomal protein uL2c / Ribosomal protein CS-L4


Mass: 29853.623 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P06509

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S ribosomal protein L11, chloroplastic / plastid ribosomal protein uL11c / CL11


Mass: 23689.980 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P31164

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S ribosomal protein L13, chloroplastic / plastid ribosomal protein uL13c / CL13


Mass: 28211.629 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P12629

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S ribosomal protein L14, chloroplastic / plastid ribosomal protein uL14c / Ribosomal protein CS-L29


Mass: 13484.741 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P09596

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)50S ribosomal protein L16, chloroplastic / plastid ribosomal protein uL16c / Ribosomal protein CS-L24


Mass: 15328.068 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P17353

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L19, chloroplastic / plastid ribosomal protein bL19c / CL19


Mass: 26121.254 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P82413

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L20, chloroplastic / plastid ribosomal protein bL20c


Mass: 15725.687 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P28803

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L21, chloroplastic / plastid ribosomal protein bL21c / CL21 / CS-L7


Mass: 28441.730 Da / Num. of mol.: 1
Details: Residues 68-81 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea / References: UniProt: P24613

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L22, chloroplastic / plastid ribosomal protein uL22c / Ribosomal protein CS-L13


Mass: 23292.676 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: P09594

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L23, chloroplastic / plastid ribosomal protein uL23c / PRPL23


Mass: 21832.164 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: Q9LWB5

Cellular component

Molecular function

Biological process

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Plastid ribosomal protein ... , 14 types, 14 molecules 6DEFGHIMOP...

#7: Polypeptide(L)plastid ribosomal protein cL37, PSRP5


Mass: 15694.817 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9S2M7

Cellular component

Molecular function

#12: Polypeptide(L)plastid ribosomal protein uL3c


Mass: 33034.750 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9QEC7

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)plastid ribosomal protein uL4c


Mass: 32541.645 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RVQ9

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)plastid ribosomal protein uL5c


Mass: 28182.688 Da / Num. of mol.: 1
Details: Residues 39-52 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RJX4

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)plastid ribosomal protein uL6c


Mass: 24516.748 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9R4N9

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)plastid ribosomal protein bL9c


Mass: 22038.904 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RQ91

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)plastid ribosomal protein uL10c


Mass: 26128.230 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9R3N5

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)plastid ribosomal protein uL15c


Mass: 29081.514 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9QHT0

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)plastid ribosomal protein bL17c


Mass: 14577.172 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RLJ4

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)plastid ribosomal protein uL18c


Mass: 18410.205 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9QQ60

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)plastid ribosomal protein uL24c


Mass: 21417.945 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9QFU9

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)plastid ribosomal protein bL27c


Mass: 21366.447 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9R4I2

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)plastid ribosomal protein bL28c


Mass: 16460.488 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9RD02

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)plastid ribosomal protein uL29c


Mass: 19083.385 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: UniProt: A0A0K9R7W8

Cellular component

Molecular function

Biological process

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RNA chain , 4 types, 4 molecules ABWz

#9: RNA chain23S ribosomal RNA / plastid 23S rRNA


Mass: 911344.250 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: GenBank: 7636084
#10: RNA chain5S ribosomal RNA / plastid 5S rRNA


Mass: 39014.184 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea
#31: RNA chain4.5S ribosomal RNA / plastid 4.5S rRNA


Mass: 34334.488 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea / References: GenBank: 12299
#35: RNA chainE-site tRNA


Mass: 589.430 Da / Num. of mol.: 1 / Details: CA-3' end of E-site tRNA / Source: (natural) Spinacia oleracea

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Non-polymers , 2 types, 503 molecules

#36: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn
#37: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 501 / Formula: Mg

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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, 28, 29, 30, 31, 32, 33, 34, 35
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 154332 / Symmetry type: POINT
Atomic model buildingOverall b value: 56.9 / 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
10.24710.23430.23463.250212.3024135116508582.5099.940.441.0626.150.901.11MLHLFLAT BULK SOLVENT MODEL
ELECTRON MICROSCOPY
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008103202
ELECTRON MICROSCOPYf_angle_d1.100154296
ELECTRON MICROSCOPYf_dihedral_angle_d16.62048326
ELECTRON MICROSCOPYf_chiral_restr0.04619619
ELECTRON MICROSCOPYf_plane_restr0.0068225
Refine LS shell

Refine ID: ELECTRON MICROSCOPY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.25010.45630.46143.2870139554328100.00
3.28700.39660.36903.3257138953061100.00
3.32570.36370.35383.3662136053815100.00
3.36620.36160.34703.4089139353861100.00
3.40890.35450.33583.4537139753596100.00
3.45370.35260.32583.5010142453475100.00
3.50100.34100.31553.5510139053622100.00
3.55100.32800.30433.6041137053704100.00
3.60410.31370.29493.6604128854345100.00
3.66040.30240.28363.7204143053187100.00
3.72040.29230.27053.7846141353519100.00
3.78460.27970.26513.8534128053784100.00
3.85340.26460.25243.9275141753678100.00
3.92750.25980.24254.0077136853529100.00
4.00770.24370.23444.0948139653910100.00
4.09480.22290.22524.1901131853189100.00
4.19010.24190.21634.2949140253886100.00
4.29490.22240.20994.4110136354042100.00
4.41100.21570.20164.5408140353423100.00
4.54080.20380.19514.6874135653684100.00
4.68740.20690.18934.8549137553742100.00
4.85490.19950.18305.0493133153608100.00
5.04930.18630.17475.2792141953354100.00
5.27920.17710.16785.5575135553915100.00
5.55750.17660.16785.9057130153805100.00
5.90570.17880.16436.3617142453373100.00
6.36170.16940.16257.0020141053715100.00
7.00200.16250.15698.0152137453652100.00
8.01520.17390.161910.0984144553681100.00
10.09840.16270.1572212.756013655302499.00

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