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Entry
Database: PDB / ID: 7lpy
TitleCrystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3-prime - 5-prime exoribonucleases
ComponentsERI1 exoribonuclease 3
KeywordsHYDROLASE / HYDROLASE METAL BINDING
Function / homology
Function and homology information


exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding
Similarity search - Function
: / : / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / ERI1 exoribonuclease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsThapar, R. / Andrew, A.S. / Tainer, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Robert A. Welch Foundation United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA220430 United States
Other privateGAP Award (to R.T., J.A.T) United States
CitationJournal: To Be Published
Title: Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3' - 5' exoribonucleases
Authors: Thapar, R. / Arvai, A.S. / Tainer, J.A.
History
DepositionFeb 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERI1 exoribonuclease 3
B: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1429
Polymers50,1362
Non-polymers1,0067
Water2,846158
1
A: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5254
Polymers25,0681
Non-polymers4573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6175
Polymers25,0681
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.555, 74.639, 96.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 136 through 503)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METLYSA1 - 200
d_12ens_1AMPAMPB
d_13ens_1MNMNC
d_21ens_1METLYSE1 - 200
d_22ens_1AMPAMPF
d_23ens_1MNMNG

NCS oper: (Code: givenMatrix: (0.0219057580138, 0.116957329073, 0.992895322248), (0.205951107689, 0.971304874946, -0.118957896537), (-0.978317064661, 0.207093754331, -0.00281032192661)Vector: 46. ...NCS oper: (Code: given
Matrix: (0.0219057580138, 0.116957329073, 0.992895322248), (0.205951107689, 0.971304874946, -0.118957896537), (-0.978317064661, 0.207093754331, -0.00281032192661)
Vector: 46.8625541359, 18.1390559779, 41.4894644022)

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Components

#1: Protein ERI1 exoribonuclease 3 / Prion interactor 1 / Prion protein-interacting protein


Mass: 25068.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERI3, PINT1, PRNPIP, PRNPIP1 / Production host: Escherichia coli (E. coli)
References: UniProt: O43414, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 35% PEG 3350, 20% saturated KCl, 200 mM Imidazole / Malate buffer pH 8.0, 5mM MnCl2, 18mM AMP, 3.3 mM N-{2-[4-(thiophen-2-yl)-1H-imidazol-2-yl]ethyl}-2,3-dihydro-1,4-benzodioxine-2- ...Details: 35% PEG 3350, 20% saturated KCl, 200 mM Imidazole / Malate buffer pH 8.0, 5mM MnCl2, 18mM AMP, 3.3 mM N-{2-[4-(thiophen-2-yl)-1H-imidazol-2-yl]ethyl}-2,3-dihydro-1,4-benzodioxine-2-carboxamide (from Life Chemicals)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→37.32 Å / Num. obs: 240157 / % possible obs: 99.6 % / Redundancy: 6.54 % / Biso Wilson estimate: 39.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.16
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 5775 / CC1/2: 0.679

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XRI

2xri


Resolution: 1.85→37.32 Å / SU ML: 0.2545 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.0151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2051 3156 5.04 %
Rwork0.1789 59494 -
obs0.1802 62650 89.79 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.81 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 56 158 3436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513367
X-RAY DIFFRACTIONf_angle_d0.7944569
X-RAY DIFFRACTIONf_chiral_restr0.0495490
X-RAY DIFFRACTIONf_plane_restr0.0051576
X-RAY DIFFRACTIONf_dihedral_angle_d16.09631258
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.605110735492 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.45491070.41421910X-RAY DIFFRACTION66.79
1.88-1.910.44531130.38552025X-RAY DIFFRACTION69.87
1.91-1.940.40491040.34582125X-RAY DIFFRACTION74.47
1.94-1.970.34641170.34542231X-RAY DIFFRACTION77.16
1.97-2.010.32271210.30742236X-RAY DIFFRACTION77.94
2.01-2.050.32061270.30152346X-RAY DIFFRACTION81.97
2.05-2.090.34171240.27332425X-RAY DIFFRACTION82.79
2.09-2.130.26971270.27322428X-RAY DIFFRACTION85.17
2.13-2.180.21671350.25642470X-RAY DIFFRACTION85.75
2.18-2.240.27621360.22782613X-RAY DIFFRACTION90.64
2.24-2.30.3061410.2332667X-RAY DIFFRACTION92.55
2.3-2.370.26521400.22312733X-RAY DIFFRACTION94.6
2.37-2.440.24391440.21562767X-RAY DIFFRACTION95.98
2.44-2.530.27331510.21082819X-RAY DIFFRACTION97.63
2.53-2.630.22271530.21172811X-RAY DIFFRACTION97.98
2.63-2.750.2031510.1952844X-RAY DIFFRACTION98.49
2.75-2.90.26341500.21442814X-RAY DIFFRACTION97.73
2.9-3.080.25351580.20422878X-RAY DIFFRACTION99.44
3.08-3.310.24681510.18842864X-RAY DIFFRACTION99.6
3.32-3.650.20921510.16782875X-RAY DIFFRACTION99.93
3.65-4.180.15021590.14172866X-RAY DIFFRACTION99.38
4.18-5.260.16711460.12562869X-RAY DIFFRACTION99.97
5.26-37.320.13071500.13942878X-RAY DIFFRACTION99.51

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