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- PDB-5dmr: Crystal Structure of C-terminal domain of mouse eRF1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 5dmr
TitleCrystal Structure of C-terminal domain of mouse eRF1 in complex with RNase H domain of RT of Moloney Murine Leukemia Virus
Components
  • Eukaryotic peptide chain release factor subunit 1
  • Reverse transcriptase/ribonuclease H p80
KeywordsHYDROLASE/TRANSLATION / eRF1 / RT / complex / HYDROLASE-TRANSLATION complex
Function / homology
Function and homology information


Eukaryotic Translation Termination / Protein hydroxylation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / retroviral 3' processing activity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation termination factor activity / translation release factor complex / host cell late endosome membrane / regulation of translational termination / translation release factor activity ...Eukaryotic Translation Termination / Protein hydroxylation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / retroviral 3' processing activity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation termination factor activity / translation release factor complex / host cell late endosome membrane / regulation of translational termination / translation release factor activity / DNA catabolic process / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / translational termination / cytosolic ribosome / protein-DNA complex / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 ...Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / : / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / 50S ribosomal protein L30e-like / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesMoloney murine leukemia virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, X. / Song, H.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus
Authors: Tang, X. / Zhu, Y. / Baker, S.L. / Bowler, M.W. / Chen, B.J. / Chen, C. / Hogg, J.R. / Goff, S.P. / Song, H.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Reverse transcriptase/ribonuclease H p80
B: Eukaryotic peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)37,5442
Polymers37,5442
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-5 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.630, 63.862, 60.431
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Reverse transcriptase/ribonuclease H p80 / RT


Mass: 18766.250 Da / Num. of mol.: 1 / Fragment: RNase H domain, UNP residues 1159-1330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus (isolate Shinnick)
Strain: isolate Shinnick / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, ribonuclease H
#2: Protein Eukaryotic peptide chain release factor subunit 1 / eRF1


Mass: 18777.975 Da / Num. of mol.: 1 / Fragment: C-terminal residues 276-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etf1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BWY3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 18 % ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. obs: 8469 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 23.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HB5 and 1DT9

2hb5

1dt9


Resolution: 2.8→59.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 16.158 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28032 431 5.1 %RANDOM
Rwork0.20693 ---
obs0.2107 8037 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.8→59.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 0 4 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192074
X-RAY DIFFRACTIONr_bond_other_d0.0020.022014
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9672794
X-RAY DIFFRACTIONr_angle_other_deg0.98634636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2835254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72924.62493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.45515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3721511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02452
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4637.1811034
X-RAY DIFFRACTIONr_mcbond_other5.4647.1771033
X-RAY DIFFRACTIONr_mcangle_it8.16610.7421282
X-RAY DIFFRACTIONr_mcangle_other8.16310.7461283
X-RAY DIFFRACTIONr_scbond_it5.8977.871039
X-RAY DIFFRACTIONr_scbond_other5.8947.8721040
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.40611.5241512
X-RAY DIFFRACTIONr_long_range_B_refined12.44456.2292232
X-RAY DIFFRACTIONr_long_range_B_other12.44356.2242231
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 21 -
Rwork0.251 614 -
obs--99.69 %

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