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- PDB-5myj: Structure of 70S ribosome from Lactococcus lactis -

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Entry
Database: PDB / ID: 5myj
TitleStructure of 70S ribosome from Lactococcus lactis
DescriptorRibosome hibernation promotion factor/RNA Complex
(30S ribosomal protein ...) x 20
(50S ribosomal protein ...) x 27
KeywordsRIBOSOME / ribosome / 70S / lactoccocus lactis / Cryo-EM
Specimen sourceLactococcus lactis subsp. cremoris mg1363 / bacteria / lactic acid bacteria
Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
MethodElectron microscopy (5.6 Å resolution / Particle / Single particle)
AuthorsFranken, L.E. / Oostergetel, G.T. / Pijning, T. / Puri, P. / Boekema, E.J. / Poolman, B. / Guskov, A.
CitationNat Commun, 2017, 8, 722-722

Nat Commun, 2017, 8, 722-722 Yorodumi Papers
A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
Linda E Franken / Gert T Oostergetel / Tjaard Pijning / Pranav Puri / Valentina Arkhipova / Egbert J Boekema / Bert Poolman / Albert Guskov

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 26, 2017 / Release: Oct 11, 2017

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein S21
B0: 50S ribosomal protein L28
B1: 50S ribosomal protein L29
B2: 50S ribosomal protein L30
B3: 50S ribosomal protein L31 type B
B4: 50S ribosomal protein L32
B5: 50S ribosomal protein L33 3
B6: 50S ribosomal protein L34
B7: 50S ribosomal protein L35
B8: 50S ribosomal protein L36
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BM: 50S ribosomal protein L13
BN: 50S ribosomal protein L14
BO: 50S ribosomal protein L15
BP: 50S ribosomal protein L16
BQ: 50S ribosomal protein L17
BR: 50S ribosomal protein L18
BS: 50S ribosomal protein L19
BT: 50S ribosomal protein L20
BU: 50S ribosomal protein L21
BV: 50S ribosomal protein L22
BW: 50S ribosomal protein L23
BX: 50S ribosomal protein L24
BZ: 50S ribosomal protein L27
A: Ribosome hibernation promotion factor


Theoretical massNumber of molelcules
Total (without water)2,115,46251
Polyers2,115,46251
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)240680
ΔGint (kcal/M)-1878
Surface area (Å2)742030
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules AABABB

#1: RNA chain16S ribosomal RNA


Mass: 497142.344 Da / Num. of mol.: 1 / Source: (natural) Lactococcus lactis subsp. cremoris MG1363 / References: GenBank: 124491690
#31: RNA chain23S ribosomal RNA


Mass: 938591.125 Da / Num. of mol.: 1 / Source: (natural) Lactococcus lactis subsp. cremoris MG1363 / References: GenBank: 124491690
#32: RNA chain5S ribosomal RNA


Mass: 37065.969 Da / Num. of mol.: 1 / Source: (natural) Lactococcus lactis subsp. cremoris MG1363 / References: GenBank: 124491690

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30S ribosomal protein ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAK...

#2: Polypeptide(L)30S ribosomal protein S2


Mass: 28589.760 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNV0

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)30S ribosomal protein S3


Mass: 24058.795 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP9

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein S4


Mass: 23232.605 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RI10

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)30S ribosomal protein S5


Mass: 17609.285 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNN6

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S6


Mass: 11321.831 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNZ4

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein S7


Mass: 17713.443 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RP73

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein S8


Mass: 14692.106 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNN9

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein S9


Mass: 14124.289 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RP61

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)30S ribosomal protein S10


Mass: 11764.765 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNQ6

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)30S ribosomal protein S11


Mass: 13310.352 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNM8

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)30S ribosomal protein S12


Mass: 15157.884 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RP74

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S13


Mass: 13519.672 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNM9

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S14 type Z


Mass: 7151.611 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP2

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein S15


Mass: 10367.041 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RMV9

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)30S ribosomal protein S16


Mass: 10270.938 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RJS1

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein S17


Mass: 10166.831 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP6

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)30S ribosomal protein S18


Mass: 9392.087 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNZ2

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein S19


Mass: 10595.238 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNQ1

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S20


Mass: 8384.740 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RMG0

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)30S ribosomal protein S21


Mass: 7041.308 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RHW9

Cellular component

Molecular function

Biological process

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50S ribosomal protein ... , 27 types, 27 molecules B0B1B2B3B4B5B6B7B8BD...

#22: Polypeptide(L)50S ribosomal protein L28


Mass: 7187.417 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RHS3

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S ribosomal protein L29


Mass: 7874.178 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP7

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S ribosomal protein L30


Mass: 6202.401 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNN5

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L31 type B


Mass: 9366.479 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RJP7

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L32


Mass: 6681.631 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RHH0

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L33 3


Mass: 5567.652 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNR2

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L34


Mass: 5200.206 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RHL6

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L35


Mass: 7844.419 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RMR2

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L36


Mass: 4432.446 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNN0

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S ribosomal protein L2


Mass: 29641.348 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNQ2

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S ribosomal protein L3


Mass: 21956.568 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNQ5

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)50S ribosomal protein L4


Mass: 22393.461 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNQ4

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)50S ribosomal protein L5


Mass: 20034.270 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP3

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)50S ribosomal protein L6


Mass: 19313.266 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNN8

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)50S ribosomal protein L13


Mass: 16192.855 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RP62
#39: Polypeptide(L)50S ribosomal protein L14


Mass: 12944.098 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP5

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)50S ribosomal protein L15


Mass: 15376.553 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNN4

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)50S ribosomal protein L16


Mass: 15375.058 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP8

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)50S ribosomal protein L17


Mass: 14280.492 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNM6

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)50S ribosomal protein L18


Mass: 12426.203 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNN7

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)50S ribosomal protein L19


Mass: 13129.329 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RLS5

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)50S ribosomal protein L20


Mass: 13726.362 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RMR1

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)50S ribosomal protein L21


Mass: 11444.199 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RLA4

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)50S ribosomal protein L22


Mass: 12490.540 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNQ0

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)50S ribosomal protein L23


Mass: 10819.567 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNQ3
#49: Polypeptide(L)50S ribosomal protein L24


Mass: 10897.782 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RNP4

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)50S ribosomal protein L27


Mass: 10053.518 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RLA2

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 1 types, 1 molecules A

#51: Polypeptide(L)Ribosome hibernation promotion factor / HPF / Lactococcus lactis hibernation promotion factor / LIHPF


Mass: 21345.988 Da / Num. of mol.: 1
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363)
References: UniProt: A2RIX0

Cellular component

Biological process

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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: 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Lactococcus lactis
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 291.15 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
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
EM imaging opticsSph aberration corrector: Cs-corrector (CEOS, Heidelberg, Germany)

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Processing

EM software
IDNameVersionCategoryImaging IDImage processing IDFitting ID
2EPUIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7CootMODEL FITTING1
9PHENIX1.11.1MODEL REFINEMENT1
10XmippINITIAL EULER ASSIGNMENT1
11RELIONFINAL EULER ASSIGNMENT1
12RELIONCLASSIFICATION1
13RELION1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43530 / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Least-squares processHighest resolution: 5.6 Å

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