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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
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • A/T, P and E-site tRNAs
  • mRNA model
KeywordsRIBOSOME / ribosome / translation / accommodation / tRNA selection
Function / homologyRibosomal protein S19, superfamily / Ribosomal protein L5, N-terminal / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, C-terminal ...Ribosomal protein S19, superfamily / Ribosomal protein L5, N-terminal / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, C-terminal / Ribosomal protein L17 superfamily / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal L18e/L15P superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S7 domain / Ribosomal protein L13 superfamily / Ribosomal protein S21 superfamily / Ribosomal protein L35 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S16 domain superfamily / Ribosomal protein L1-like / Ribosomal protein L19 superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, C-terminal / Ribosomal protein L16, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L1, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L1, archaea / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L33 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L3, conserved site / Ribosomal protein L11, N-terminal domain / Ribosomal protein S7 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / KH domain / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S11 signature. / Ribosomal L32p protein family / Ribosomal protein S20 / Ribosomal protein L35 / S4 domain / Ribosomal L25p family / Ribosomal protein L9, N-terminal domain
Function and homology information
Specimen sourceEscherichia coli (E. coli)
Sulfolobus acidocaldarius (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9 Å resolution
AuthorsDevkota, B. / Caulfield, T.R. / Tan, R.-Z. / Harvey, S.C.
CitationJournal: To be Published
Title: The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading
Authors: 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 chain A/T, P and E-site tRNAs


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


Mass: 6078.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: PDB-4V7W
#3: RNA chain 16S rRNA


Mass: 495927.719 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: PDB-4V7W
#24: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37848.555 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 170517292
#25: RNA chain 23S rRNA / 23S ribosomal RNA


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

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

#4: Protein/peptide 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#5: Protein/peptide 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#6: Protein/peptide 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#7: Protein/peptide 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9
#8: Protein/peptide 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59
#9: Protein/peptide 30S ribosomal protein S15 /


Mass: 10319.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q8X9M2
#10: Protein/peptide 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3
#11: Protein/peptide 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#12: Protein/peptide 30S ribosomal protein S18 /


Mass: 9006.500 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#13: Protein/peptide 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3
#14: Protein/peptide 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#15: Protein/peptide 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#16: Protein/peptide 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679
#17: Protein/peptide 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#18: Protein/peptide 30S ribosomal protein S5 /


Mass: 16772.412 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#19: Protein/peptide 30S ribosomal protein S6 /


Mass: 15727.512 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#20: Protein/peptide 30S ribosomal protein S7 /


Mass: 20055.156 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#21: Protein/peptide 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q3YWV3
#22: Protein/peptide 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3
#23: Protein/peptide 30S ribosomal protein S10 /


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

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50S ribosomal protein ... , 30 types, 30 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB1B2B3B4B5B6

#26: Protein/peptide 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#27: Protein/peptide 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#28: Protein/peptide 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#29: Protein/peptide 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#30: Protein/peptide 50S ribosomal protein L17 /


Mass: 14393.657 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#31: Protein/peptide 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#32: Protein/peptide 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#33: Protein/peptide 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#34: Protein/peptide 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#35: Protein/peptide 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#36: Protein/peptide 50S ribosomal protein L23 /


Mass: 11093.047 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#37: Protein/peptide 50S ribosomal protein L2 /


Mass: 29550.166 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#38: Protein/peptide 50S ribosomal protein L24 /


Mass: 11210.069 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#39: Protein/peptide 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#40: Protein/peptide 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#41: Protein/peptide 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#42: Protein/peptide 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M9
#43: Protein/peptide 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#44: Protein/peptide 50S ribosomal protein L33 /


Mass: 6257.436 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#45: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#46: Protein/peptide 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#47: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q6
#48: Protein/peptide 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#49: Protein/peptide 50S ribosomal protein L1P / Ribosome


Mass: 23978.031 Da / Num. of mol.: 1 / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / References: UniProt: P35024
#50: Protein/peptide 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#51: Protein/peptide 50S ribosomal protein L5 /


Mass: 20202.416 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#52: Protein/peptide 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#53: Protein/peptide 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#54: Protein/peptide 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#55: Protein/peptide 50S ribosomal protein L13 /


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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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 FIELDBright-field microscopy / 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
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1
3D reconstructionMethod: Single ParticleSingle particle analysis / 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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