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

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Basic information

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 (8 A resolution / Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Aug 16, 2006 / Release: Nov 8, 2006 / Last modification: Oct 20, 2010

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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)1,428,781145
Polyers1,426,08334
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: 6332.307 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: 6257.510 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: 5397.506 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: 7181.907 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: 4377.415 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: 29248.984 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: 22277.709 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: 22121.723 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: 20202.566 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: 18801.766 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: 15789.174 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: 14763.286 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: 15822.503 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: 13320.821 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: 15008.598 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: 15312.394 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: 14393.774 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: 12794.793 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: 13028.207 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: 13396.962 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: 11586.485 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: 12253.464 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: 11093.154 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: 11078.988 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: 10713.566 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: 9015.426 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: 7286.531 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: 6423.682 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: 7887.165 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: 2121.567 Da / Num. of mol.: 1

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)SIGNAL RECOGNITION PARTICLE 54


Mass: 47362.551 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: 23968.469 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI
#9: RNA chain5S RIBOSOMAL RNA


Mass: 37848.766 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI
#10: RNA chain23S RIBOSOMAL RNA


Mass: 941613.688 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: SRP BOUND TO 70S RNCS / Aggregation state: PARTICLE
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F30
Electron gunAccelerating voltage: 300 kV
Electron lensMode: BRIGHT FIELD
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: SPIDER
EM single particle entitySymmetry type: ASYMMETRIC
Least-squares processHighest resolution: 8 A
Refine hist #LASTHighest resolution: 8 A
Number of atoms included #LASTProtein: 29643 / Nucleic acid: 65092 / Ligand: 111 / Solvent: 512 / Total: 95358

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