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- PDB-4v66: Structure of the E. coli ribosome and the tRNAs in Post-accommoda... -

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Entry
Database: PDB / ID: 4v66
TitleStructure of the E. coli ribosome and the tRNAs in Post-accommodation state
DescriptorRibosome
KeywordsRIBOSOME / ribosome / translation / accommodation / tRNA selection
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Sulfolobus acidocaldarius / archaea / thermophilic / スルホロブス・アシドカルダリウス
MethodElectron microscopy (9 Å resolution / Particle / Single particle)
AuthorsDevkota, B. / Caulfield, T.R. / Tan, R.-Z. / Harvey, S.C.
CitationTo be Published

To be Published Search PubMed
The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading
Devkota, B. / Caulfield, T.R. / Tan, R.-Z. / Harvey, S.C.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 3, 2008 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Mar 25, 2015Structure modelOther

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Assembly

Deposited unit
AA: A/T, P and E-site tRNAs
AP: A/T, P and E-site tRNAs
AE: A/T, P and E-site tRNAs
AM: mRNA model
A1: 16S rRNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S11
AD: 30S ribosomal protein S12
AF: 30S ribosomal protein S13
AG: 30S ribosomal protein S14
AH: 30S ribosomal protein S15
AI: 30S ribosomal protein S16
AJ: 30S ribosomal protein S17
AK: 30S ribosomal protein S18
AL: 30S ribosomal protein S19
AN: 30S ribosomal protein S20
AO: 30S ribosomal protein S3
AQ: 30S ribosomal protein S21
AR: 30S ribosomal protein S4
AS: 30S ribosomal protein S5
AT: 30S ribosomal protein S6
AU: 30S ribosomal protein S7
AV: 30S ribosomal protein S8
AW: 30S ribosomal protein S9
AX: 30S ribosomal protein S10
BA: 5S rRNA
BB: 23S rRNA
BC: 50S ribosomal protein L25
BD: 50S ribosomal protein L14
BE: 50S ribosomal protein L15
BF: 50S ribosomal protein L16
BG: 50S ribosomal protein L17
BH: 50S ribosomal protein L18
BI: 50S ribosomal protein L19
BJ: 50S ribosomal protein L20
BK: 50S ribosomal protein L21
BL: 50S ribosomal protein L22
BM: 50S ribosomal protein L23
BN: 50S ribosomal protein L2
BO: 50S ribosomal protein L24
BP: 50S ribosomal protein L27
BQ: 50S ribosomal protein L29
BR: 50S ribosomal protein L30
BS: 50S ribosomal protein L31
BT: 50S ribosomal protein L32
BU: 50S ribosomal protein L33
BV: 50S ribosomal protein L34
BW: 50S ribosomal protein L35
BX: 50S ribosomal protein L36
BY: 50S ribosomal protein L3
BZ: 50S ribosomal protein L1P
B1: 50S ribosomal protein L4
B2: 50S ribosomal protein L5
B3: 50S ribosomal protein L6
B4: 50S ribosomal protein L9
B5: 50S ribosomal protein L11
B6: 50S ribosomal protein L13


Theoretical massNumber of molelcules
Total (without water)2,242,44657
Polyers2,242,44657
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 7 molecules AAAPAEAMA1BABB

#1: RNA chainA/T, P and E-site tRNAs


Mass: 24518.570 Da / Num. of mol.: 3 / Source: (natural) Escherichia coli / References: PDB: 4V7W
#2: RNA chainmRNA model


Mass: 6078.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: PDB: 4V7W
#3: RNA chain16S rRNA


Mass: 495927.719 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: PDB: 4V7W
#24: RNA chain5S rRNA


Mass: 37848.555 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 170517292
#25: RNA chain23S rRNA


Mass: 941306.188 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 169887498

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

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


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7V0

Cellular component

Molecular function

Biological process

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


Mass: 13870.975 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7R9

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#6: Polypeptide(L)30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

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


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7S9

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG59

Cellular component

Molecular function

Biological process

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


Mass: 10319.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: Q8X9M2

Cellular component

Molecular function

Biological process

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


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7T3

Cellular component

Molecular function

Biological process

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


Mass: 9724.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG63

Cellular component

Molecular function

Biological process

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


Mass: 9006.500 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7T7

Cellular component

Molecular function

Biological process

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


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7U3

Cellular component

Molecular function

Biological process

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


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7U7

Cellular component

Molecular function

Biological process

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


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7V3

Cellular component

Molecular function

Biological process

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


Mass: 8524.039 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P68679

Cellular component

Molecular function

Biological process

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


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7V8

Cellular component

Molecular function

Biological process

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


Mass: 16772.412 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7W1

Cellular component

Molecular function

Biological process

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


Mass: 15727.512 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02358

Cellular component

Molecular function

Biological process

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


Mass: 20055.156 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02359

Cellular component

Molecular function

Biological process

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


Mass: 14146.557 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: Q3YWV3

Cellular component

Molecular function

Biological process

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


Mass: 14886.270 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7X3

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#23: Polypeptide(L)30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7R5

Cellular component

Molecular function

Biological process

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50S ribosomal protein ... , 30 types, 30 molecules BCBDBEBFBGBHBIBJBKBL...

#26: Polypeptide(L)50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P68919

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADY3

Cellular component

Molecular function

Biological process

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


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02413

Cellular component

Molecular function

Biological process

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


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADY7

Cellular component

Molecular function

Biological process

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


Mass: 14393.657 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG44

Cellular component

Molecular function

Biological process

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


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0C018

Cellular component

Molecular function

Biological process

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


Mass: 13159.278 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7K6

Cellular component

Molecular function

Biological process

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


Mass: 13528.024 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L3

Cellular component

Molecular function

Biological process

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


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG48

Cellular component

Molecular function

Biological process

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


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P61175

Cellular component

Molecular function

Biological process

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


Mass: 11093.047 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADZ0

Cellular component

Molecular function

Biological process

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


Mass: 29550.166 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60422

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)50S ribosomal protein L24


Mass: 11210.069 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60624

Cellular component

Molecular function

Biological process

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


Mass: 9146.540 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L8

Cellular component

Molecular function

Biological process

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


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M6

Cellular component

Molecular function

Biological process

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


Mass: 6554.820 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG51

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)50S ribosomal protein L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M9

Cellular component

Molecular function

Biological process

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


Mass: 6463.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7N4

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)50S ribosomal protein L33


Mass: 6257.436 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7N9

Cellular component

Molecular function

Biological process

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


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7P5

Cellular component

Molecular function

Biological process

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


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q1

Cellular component

Molecular function

Biological process

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


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q6

Cellular component

Molecular function

Biological process

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


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60438

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)50S ribosomal protein L1P


Mass: 23978.031 Da / Num. of mol.: 1 / Source: (natural) Sulfolobus acidocaldarius / References: UniProt: P35024

Cellular component

Molecular function

Biological process

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


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60723

Cellular component

Molecular function

Biological process

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


Mass: 20202.416 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P62399

Cellular component

Molecular function

Biological process

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


Mass: 18932.791 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG55

Cellular component

Molecular function

Biological process

#53: Polypeptide(L)50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7R1

Cellular component

Molecular function

Biological process

#54: Polypeptide(L)50S ribosomal protein L11


Mass: 14894.362 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

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


Mass: 15822.360 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AA10

Cellular component

Molecular function

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: E. coli ribosome in post-accommodation state / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1Yup.scxMODEL FITTING
2SPIDERRECONSTRUCTION
SymmetryPoint symmetry: C1
3D reconstructionMethod: Single Particle / Resolution: 9 Å / Number of particles: 52181 / Nominal pixel size: 2.82 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--Flexible fitting / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: cross-correlation
Atomic model building
IDPDB-ID 3D fitting ID
12I2P1
21EHZ1
Number of atoms included #LASTProtein: 18529 / Nucleic acid: 38047 / Ligand: 0 / Solvent: 0 / Total: 56576

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