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- PDB-1rq0: Crystal structure of peptide releasing factor 1 -

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Basic information

Entry
Database: PDB / ID: 1rq0
TitleCrystal structure of peptide releasing factor 1
ComponentsPeptide chain release factor 1
Keywordspeptide release factor 1 / crystal / ribosome / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


translation release factor activity, codon specific / cytoplasm
Similarity search - Function
Helix Hairpins - #160 / Alpha-Beta Plaits - #1660 / Peptide chain release factor 1 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I ...Helix Hairpins - #160 / Alpha-Beta Plaits - #1660 / Peptide chain release factor 1 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I / RF-1 domain / Helix Hairpins / Double Stranded RNA Binding Domain / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide chain release factor 1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsShin, D.H. / Brandsen, J. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J Mol Biol / Year: 2004
Title: Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome.
Authors: Dong Hae Shin / Jeroen Brandsen / Jaru Jancarik / Hisao Yokota / Rosalind Kim / Sung-Hou Kim /
Abstract: We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65 Angstrom resolution by selenomethionine single-wavelength anomalous ...We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65 Angstrom resolution by selenomethionine single-wavelength anomalous dispersion (SAD) techniques. RF1 is a protein that recognizes stop codons and promotes the release of a nascent polypeptide from tRNA on the ribosome. Selenomethionine-labeled RF1 crystallized in space group P2(1) with three monomers per asymmetric unit. It has approximate dimensions of 75 Angstrom x 70 Angstrom x 45 Angstrom and is composed of four domains. The overall fold of each RF1 domain shows almost the same topology with Escherichia coli RF2, except that the RF1 N-terminal domain is shorter and the C-terminal domain is longer than that of RF2. The N-terminal domain of RF1 indicates a rigid-body movement relative to that of RF2 with an angle of approximately 90 degrees. Including these features, RF1 has a tripeptide anticodon PVT motif instead of the SPF motif of RF2, which confers the specificity towards the stop codons. The analyses of three molecules in the asymmetric unit and comparison with RF2 revealed the presence of dynamic movement of domains I and III, which are anchored to the central domain by hinge loops. The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide chain release factor 1
B: Peptide chain release factor 1
C: Peptide chain release factor 1


Theoretical massNumber of molelcules
Total (without water)119,1473
Polymers119,1473
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.900, 137.230, 80.930
Angle α, β, γ (deg.)90.00, 106.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide chain release factor 1 / RF-1


Mass: 39715.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: PRFA, TM1363 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X183
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, KCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2001
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.65→52.7 Å / Num. obs: 30338 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 7.3 Å2 / Net I/σ(I): 12.9
Reflection shellResolution: 2.65→2.7 Å / % possible all: 84.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→19.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 67931.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2680 10 %RANDOM
Rwork0.216 ---
all0.224 61466 --
obs0.216 26687 84.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2769 Å2 / ksol: 0.330232 e/Å3
Displacement parametersBiso mean: 49.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å20 Å213.16 Å2
2---7.71 Å20 Å2
3---3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7798 0 0 204 8002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 308 10.2 %
Rwork0.238 2706 -
obs--57.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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