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- PDB-2j37: MODEL OF MAMMALIAN SRP BOUND TO 80S RNCS -

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Entry
Database: PDB / ID: 2j37
TitleMODEL OF MAMMALIAN SRP BOUND TO 80S RNCS
Descriptor60S RIBOSOMAL PROTEIN L23
SIGNAL SEQUENCE
(RIBOSOMAL PROTEIN ...) x 2
(SIGNAL RECOGNITION PARTICLE ...) x 2
KeywordsRIBOSOME / SRP / TRANSLATION/RNA
Specimen sourceTriticum sp. / plant / WHEAT / image: Triticum aestivum
Triticum sp / plant / WHEAT / image: Triticum aestivum
Canis sp. / mammal / image: Canis lupus familiaris
Homo sapiens / human
Haloarcula marismortui / archaea / Halophile / ハロアーキュラ・マリスモーツイ
MethodElectron microscopy (8.7 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 Yorodumi Papers
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 18, 2006 / Release: Nov 8, 2006
RevisionDateData content typeGroupProviderType
1.0Nov 8, 2006Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
4: 60S RIBOSOMAL PROTEIN L23
5: RIBOSOMAL PROTEIN L35
6: RIBOSOMAL PROTEIN L31
A: SRP RNA
B: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN (SRP19)
S: SIGNAL SEQUENCE
W: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54)
Z: RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)248,0048
Polyers248,0048
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11800
ΔGint (kcal/M)-45.2
Surface area (Å2)123400
MethodPQS

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Components

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Polypeptide(L) , 2 types, 2 molecules 4S

#1: Polypeptide(L)60S RIBOSOMAL PROTEIN L23


Mass: 16920.203 Da / Num. of mol.: 1 / Source: (natural) TRITICUM SP. / References: UniProt: 2J37

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)SIGNAL SEQUENCE


Mass: 1992.362 Da / Num. of mol.: 1

Cellular component

Molecular function

Biological process

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RIBOSOMAL PROTEIN ... , 2 types, 2 molecules 56

#2: Polypeptide(L)RIBOSOMAL PROTEIN L35


Mass: 14401.041 Da / Num. of mol.: 1 / Source: (natural) TRITICUM SP. / References: UniProt: Q8L805

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)RIBOSOMAL PROTEIN L31


Mass: 14152.365 Da / Num. of mol.: 1 / Source: (natural) TRITICUM SP

Cellular component

Molecular function

Biological process

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RNA chain , 2 types, 2 molecules AZ

#4: RNA chainSRP RNA


Mass: 41504.750 Da / Num. of mol.: 1 / Source: (natural) CANIS SP.
#8: RNA chainRIBOSOMAL RNA


Mass: 90695.906 Da / Num. of mol.: 1 / Source: (natural) HALOARCULA MARISMORTUI

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SIGNAL RECOGNITION PARTICLE ... , 2 types, 2 molecules BW

#5: Polypeptide(L)SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN (SRP19)


Mass: 12561.688 Da / Num. of mol.: 1 / Source: (natural) HOMO SAPIENS / References: UniProt: P09132

Cellular component

Molecular function

Biological process

  • cotranslational protein targeting to membrane (GO: 0006613)
  • response to drug (GO: 0042493)
  • SRP-dependent cotranslational protein targeting to membrane (GO: 0006614)
  • SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO: 0006617)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)
#7: Polypeptide(L)SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54)


Mass: 55775.672 Da / Num. of mol.: 1 / Source: (natural) CANIS SP. / References: UniProt: P61010

Cellular component

Molecular function

Biological process

  • protein targeting to ER (GO: 0045047)
  • response to drug (GO: 0042493)
  • SRP-dependent cotranslational protein targeting to membrane (GO: 0006614)
  • SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO: 0006617)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)

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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 80S 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 / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C1
3D reconstructionResolution: 8.7 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: 6354 / Nucleic acid: 8756 / Ligand: 0 / Solvent: 0 / Total: 15110

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