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- PDB-2j28: MODEL OF E. COLI SRP BOUND TO 70S RNCS -

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Entry
Database: PDB / ID: 2j28
TitleMODEL OF E. COLI SRP BOUND TO 70S RNCS
DescriptorSIGNAL SEQUENCE
SIGNAL RECOGNITION PARTICLE 54
(50S RIBOSOMAL PROTEIN ...) x 28
KeywordsRIBOSOME / PROTEIN-RNA COMPLEX / SIGNAL RECOGNITION PARTICLE
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (9.5 Å resolution / Particle / Single particle)
AuthorsHalic, M. / Blau, M. / Becker, T. / Mielke, T. / Pool, M.R. / Wild, K. / Sinning, I. / Beckmann, R.
CitationNature, 2006, 444, 507-511

Nature, 2006, 444, 507-511 StrPapers
Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
Mario Halic / Michael Blau / Thomas Becker / Thorsten Mielke / Martin R Pool / Klemens Wild / Irmgard Sinning / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 16, 2006 / Release: Nov 8, 2006
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 8, 2006Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Apr 19, 2017Structure modelOther
1.4Aug 30, 2017Structure modelData collection / Source and taxonomyem_image_scans / entity_src_gen_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name

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Assembly

Deposited unit
0: 50S RIBOSOMAL PROTEIN L32
1: 50S RIBOSOMAL PROTEIN L33
2: 50S RIBOSOMAL PROTEIN L34
3: 50S RIBOSOMAL PROTEIN L35
4: 50S RIBOSOMAL PROTEIN L36
7: SIGNAL SEQUENCE
8: 4.5S SIGNAL RECOGNITION PARTICLE RNA
9: SIGNAL RECOGNITION PARTICLE 54
A: 5S RIBOSOMAL RNA
B: 23S RIBOSOMAL RNA
C: 50S RIBOSOMAL PROTEIN L2
D: 50S RIBOSOMAL PROTEIN L3
E: 50S RIBOSOMAL PROTEIN L4
F: 50S RIBOSOMAL PROTEIN L5
G: 50S RIBOSOMAL PROTEIN L6
H: 50S RIBOSOMAL PROTEIN L9
I: 50S RIBOSOMAL PROTEIN L11
J: 50S RIBOSOMAL PROTEIN L13
K: 50S RIBOSOMAL PROTEIN L14
L: 50S RIBOSOMAL PROTEIN L15
M: 50S RIBOSOMAL PROTEIN L16
N: 50S RIBOSOMAL PROTEIN L17
O: 50S RIBOSOMAL PROTEIN L18
P: 50S RIBOSOMAL PROTEIN L19
Q: 50S RIBOSOMAL PROTEIN L20
R: 50S RIBOSOMAL PROTEIN L21
S: 50S RIBOSOMAL PROTEIN L22
T: 50S RIBOSOMAL PROTEIN L23
U: 50S RIBOSOMAL PROTEIN L24
V: 50S RIBOSOMAL PROTEIN L25
W: 50S RIBOSOMAL PROTEIN L27
X: 50S RIBOSOMAL PROTEIN L29
Y: 50S RIBOSOMAL PROTEIN L30
Z: 50S RIBOSOMAL PROTEIN L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,428,776145
Polyers1,426,07834
Non-polymers2,698111
Water9,224512
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

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50S RIBOSOMAL PROTEIN ... , 29 types, 29 molecules 01234CDEFG...

#1: Polypeptide(L)50S RIBOSOMAL PROTEIN L32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7N4

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)50S RIBOSOMAL PROTEIN L33


Mass: 6257.436 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7N9

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)50S RIBOSOMAL PROTEIN L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7P5

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)50S RIBOSOMAL PROTEIN L35


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7Q2

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)50S RIBOSOMAL PROTEIN L36


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7Q6

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)50S RIBOSOMAL PROTEIN L2


Mass: 29248.758 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P60422

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)50S RIBOSOMAL PROTEIN L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P60438

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)50S RIBOSOMAL PROTEIN L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P60723

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)50S RIBOSOMAL PROTEIN L5


Mass: 20202.416 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P62399

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)50S RIBOSOMAL PROTEIN L6


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0AG55

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)50S RIBOSOMAL PROTEIN L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7R1

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)50S RIBOSOMAL PROTEIN L11


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S RIBOSOMAL PROTEIN L13


Mass: 15822.360 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0AA10

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S RIBOSOMAL PROTEIN L14


Mass: 13320.714 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0ADY3

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S RIBOSOMAL PROTEIN L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P02413

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)50S RIBOSOMAL PROTEIN L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0ADY7

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)50S RIBOSOMAL PROTEIN L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0AG44

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S RIBOSOMAL PROTEIN L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0C018

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S RIBOSOMAL PROTEIN L19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7K6

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S RIBOSOMAL PROTEIN L20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7L3

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S RIBOSOMAL PROTEIN L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0AG48

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S RIBOSOMAL PROTEIN L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P61175

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S RIBOSOMAL PROTEIN L23


Mass: 11093.047 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0ADZ0

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S RIBOSOMAL PROTEIN L24


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P60624

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S RIBOSOMAL PROTEIN L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P68919

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S RIBOSOMAL PROTEIN L27


Mass: 9015.344 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7L8

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S RIBOSOMAL PROTEIN L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7M6

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S RIBOSOMAL PROTEIN L30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0AG51

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S RIBOSOMAL PROTEIN L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0A7M9

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 2 types, 2 molecules 79

#6: Polypeptide(L)SIGNAL SEQUENCE


Mass: 2121.542 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)SIGNAL RECOGNITION PARTICLE 54


Mass: 47362.168 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI / References: UniProt: P0AGD7

Cellular component

Molecular function

Biological process

  • protein targeting to membrane (GO: 0006612)
  • SRP-dependent cotranslational protein targeting to membrane (GO: 0006614)

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RNA chain , 3 types, 3 molecules 8AB

#7: RNA chain4.5S SIGNAL RECOGNITION PARTICLE RNA


Mass: 23968.311 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI
#9: RNA chain5S RIBOSOMAL RNA


Mass: 37848.555 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI
#10: RNA chain23S RIBOSOMAL RNA


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI

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Non-polymers , 2 types, 623 molecules

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


Mass: 24.305 Da / Num. of mol.: 111 / Formula: Mg
#36: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Formula: H2O

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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: SRP BOUND TO 70S RNCS / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: RECONSTRUCTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT
Least-squares processHighest resolution: 8 Å
Refine hist #LASTHighest resolution: 8 Å
Number of atoms included #LASTProtein: 29643 / Nucleic acid: 65092 / Ligand: 111 / Solvent: 512 / Total: 95358

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