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- PDB-5dmq: Crystal structure of mouse eRF1 in complex with Reverse Transcrip... -

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Basic information

Entry
Database: PDB / ID: 5dmq
TitleCrystal structure of mouse eRF1 in complex with Reverse Transcriptase (RT) of Moloney Murine Leukemia Virus
Components
  • Eukaryotic peptide chain release factor subunit 1
  • Reverse transcriptase/ribonuclease H p80
KeywordsTRANSFERASE / HYDROLASE/TRANSLATION / complex / eRF1 / RT / 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) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / retroviral 3' processing activity / 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) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / retroviral 3' processing activity / 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 / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase 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
RNase H-like domain found in reverse transcriptase / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / 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 ...RNase H-like domain found in reverse transcriptase / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / 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 / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / 50S ribosomal protein L30e-like / RNase H / 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 / Alpha-Beta Plaits / Roll / 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 / Resolution: 4 Å
AuthorsTang, T. / 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 / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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

Downloads & links

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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)121,2372
Polymers121,2372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-4 kcal/mol
Surface area53960 Å2
Unit cell
Length a, b, c (Å)92.653, 92.653, 289.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 72144.055 Da / Num. of mol.: 1
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, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Protein Eukaryotic peptide chain release factor subunit 1 / eRF1


Mass: 49092.742 Da / Num. of mol.: 1
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

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M magnesium chloride, 0.1 M HEPES pH 7.5, 20 % polyacrylic acid sodium salt 5100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→96.65 Å / Num. obs: 12901 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 4→4.1 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PHASERphasing
Cootmodel building
RefinementResolution: 4→96.65 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 82.814 / SU ML: 1.025 / Cross valid method: THROUGHOUT / ESU R Free: 0.965 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29523 637 5 %RANDOM
Rwork0.24086 ---
obs0.24367 12209 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 227.182 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 4→96.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7877 0 0 0 7877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198047
X-RAY DIFFRACTIONr_bond_other_d0.0020.027900
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.97610904
X-RAY DIFFRACTIONr_angle_other_deg0.961318193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1155996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73624.169343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.374151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5641549
X-RAY DIFFRACTIONr_chiral_restr0.0710.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218985
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021780
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 51 -
Rwork0.42 849 -
obs--99.89 %

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