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- PDB-1ry1: Structure of the signal recognition particle interacting with the... -

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Basic information

Entry
Database: PDB / ID: 1ry1
TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome
Descriptorsignal receptor proteins/RNA Complex
KeywordsTRANSLATION / signal recognition particle / RNA binding
Specimen sourceHomo sapiens / human
Thermus aquaticus / bacteria / thermophilic / サームス・エクアティカス
Mus musculus / mammal / house mouse / ハツカネズミ, はつかねずみ /
Tursiops truncatus / mammal / bottlenosed dolphin / バンドウイルカ, ばんどういるか /
MethodElectron microscopy (12 Å resolution / Particle / Single particle)
AuthorsHalic, M. / Becker, T. / Pool, M.R. / Spahn, C.M. / Grassucci, R.A. / Frank, J. / Beckmann, R.
CitationNature, 2004, 427, 808-814

Nature, 2004, 427, 808-814 StrPapers
Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
Mario Halic / Thomas Becker / Martin R Pool / Christian M T Spahn / Robert A Grassucci / Joachim Frank / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 19, 2003 / Release: Apr 20, 2004
RevisionDateData content typeGroupProviderType
1.0Apr 20, 2004Structure modelrepositoryInitial release
1.1Oct 16, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
E: ALU DOMAIN (RNA FRAGMENTS)
A: ALU DOMAIN (SRP9, SRP14 + RNA)
M: fragment of 7S RNA
N: RNA (31-MER)
O: RNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')
P: RNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')
Q: RNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')
R: RNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')
C: PROTEIN (Signal recognition particle 9 kDa protein)
D: PROTEIN (Signal recognition particle 14 kDa protein)
B: PROTEIN (Signal recognition particle 19 kDa protein)
U: Signal recognition particle protein
W: Signal recognition particle 54 kDa protein
S: Rhodopsin


Theoretical massNumber of molelcules
Total (without water)179,84614
Polyers179,84614
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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ALU DOMAIN ... , 2 types, 2 molecules EA

#1: RNA chainALU DOMAIN (RNA FRAGMENTS)


Mass: 16277.622 Da / Num. of mol.: 1
#2: RNA chainALU DOMAIN (SRP9, SRP14 + RNA)


Mass: 41566.715 Da / Num. of mol.: 1

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RNA chain , 6 types, 6 molecules MNOPQR

#3: RNA chainfragment of 7S RNA


Mass: 8784.278 Da / Num. of mol.: 1
#4: RNA chainRNA (31-MER)


Mass: 9807.837 Da / Num. of mol.: 1
#5: RNA chainRNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')


Mass: 7695.542 Da / Num. of mol.: 1
#6: RNA chainRNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')


Mass: 6325.847 Da / Num. of mol.: 1
#7: RNA chainRNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')


Mass: 3844.320 Da / Num. of mol.: 1
#8: RNA chainRNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')


Mass: 3804.296 Da / Num. of mol.: 1

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PROTEIN (Signal recognition particle ... , 3 types, 3 molecules CDB

#9: Polypeptide(L)PROTEIN (Signal recognition particle 9 kDa protein) / SRP9


Mass: 9996.567 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P49458

Cellular component

Molecular function

Biological process

  • negative regulation of translational elongation (GO: 0045900)
  • SRP-dependent cotranslational protein targeting to membrane (GO: 0006614)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)
#10: Polypeptide(L)PROTEIN (Signal recognition particle 14 kDa protein) / SRP14 / 18 kDa ALU RNA binding protein


Mass: 12114.235 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P37108

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)PROTEIN (Signal recognition particle 19 kDa protein) / SRP19


Mass: 12561.688 Da / Num. of mol.: 1 / Source: (gene. exp.) 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)

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Signal recognition particle ... , 2 types, 2 molecules UW

#12: Polypeptide(L)Signal recognition particle protein / Fifty-four homolog


Mass: 32472.508 Da / Num. of mol.: 1 / Source: (gene. exp.) Thermus aquaticus / References: UniProt: O07347

Cellular component

Molecular function

Biological process

  • SRP-dependent cotranslational protein targeting to membrane (GO: 0006614)
#13: Polypeptide(L)Signal recognition particle 54 kDa protein / SRP54


Mass: 12473.440 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus / References: UniProt: P14576

Cellular component

Molecular function

Biological process

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

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Polypeptide(L) , 1 types, 1 molecules S

#14: Polypeptide(L)Rhodopsin


Mass: 2121.542 Da / Num. of mol.: 1 / Source: (gene. exp.) Tursiops truncatus / References: UniProt: O62798

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: signal recognition particle interacting with elongation-arrested ribosome
Type: RIBOSOME
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: PLUNGED INTO ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Jan 1, 2000
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 51000 / Calibrated magnification: 52000 / Nominal defocus max: 45000 nm / Nominal defocus min: 10000 nm / Cs: 2 mm
Specimen holderTemperature: 95 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 75

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Processing

EM software
IDNameCategory
1SPIDERRECONSTRUCTION
2SPIDERRECONSTRUCTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.5 CUT-OFF
Details: The chains M, N, O, P, Q and R are fragments of a double helical strand of RNA. The author maintains that some of the residues could not be modeled correctly due to limited resolution in this region.
Symmetry type: POINT
Least-squares processHighest resolution: 12 Å
Refine hist #LASTHighest resolution: 12 Å
Number of atoms included #LASTProtein: 5335 / Nucleic acid: 6459 / Ligand: 0 / Solvent: 0 / Total: 11794

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