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Entry
Database: PDB / ID: 7lpz
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


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 / SAMARIUM (III) ION / ERI1 exoribonuclease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsThapar, R. / Andrew, A.S. / Tainer, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Robert A. Welch Foundation
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 1.2Nov 13, 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)51,5249
Polymers50,1362
Non-polymers1,3887
Water5,927329
1
A: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7164
Polymers25,0681
Non-polymers6483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8085
Polymers25,0681
Non-polymers7404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.727, 74.785, 96.879
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_1(chain "A" and (resid 135 through 181 or resid 183 through 285 or resid 287 through 503))
d_2ens_1(chain "B" and (resid 135 through 181 or resid 183 through 285 or resid 287 through 503))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERGLUA1 - 47
d_12ens_1THRCYSA51 - 153
d_13ens_1PROLYSA157 - 205
d_14ens_1AMPAMPB
d_15ens_1SMSMC
d_21ens_1SERGLUE1 - 47
d_22ens_1THRCYSE49 - 151
d_23ens_1PROLYSE153 - 201
d_24ens_1AMPAMPF
d_25ens_1SMSMG

NCS oper: (Code: givenMatrix: (0.0120605054072, 0.115438158984, 0.993241448823), (0.205984769455, 0.971722321892, -0.115438312049), (-0.978480873069, 0.205984855235, -0.0120590402472)Vector: 47. ...NCS oper: (Code: given
Matrix: (0.0120605054072, 0.115438158984, 0.993241448823), (0.205984769455, 0.971722321892, -0.115438312049), (-0.978480873069, 0.205984855235, -0.0120590402472)
Vector: 47.680846994, 18.069813269, 41.8797492586)

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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-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sm / 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.: 329 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 3350, 25% saturated KCl, 200 mM Imidazole / Malate buffer 8.0, 2.5 mM samarium (III) acetate, 18mM AMP, 3.3 mM N-{2-[4-(thiophen-2-yl)-1H-imidazol-2-yl]ethyl}-2,3-dihydro-1,4- ...Details: 30% PEG 3350, 25% saturated KCl, 200 mM Imidazole / Malate buffer 8.0, 2.5 mM samarium (III) acetate, 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: 1.55→37.39 Å / Num. obs: 407820 / % possible obs: 99.4 % / Redundancy: 6.56 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 1 / Net I/σ(I): 22.42
Reflection shellResolution: 1.55→1.64 Å / Num. unique obs: 63859 / CC1/2: 0.631

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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: 1.55→37.39 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.8326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 3399 3.18 %
Rwork0.1584 103467 -
obs0.1596 106866 89.42 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.83 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 56 329 3615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473393
X-RAY DIFFRACTIONf_angle_d0.77174608
X-RAY DIFFRACTIONf_chiral_restr0.0473492
X-RAY DIFFRACTIONf_plane_restr0.0044581
X-RAY DIFFRACTIONf_dihedral_angle_d13.44091267
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.533027182314 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.46271040.42353054X-RAY DIFFRACTION64.04
1.57-1.60.38831100.38763314X-RAY DIFFRACTION68.04
1.6-1.620.39011110.35073519X-RAY DIFFRACTION72.8
1.62-1.650.39821190.31573603X-RAY DIFFRACTION75.09
1.65-1.680.30951230.28763808X-RAY DIFFRACTION77.92
1.68-1.710.29911160.26123772X-RAY DIFFRACTION79.61
1.71-1.740.28291350.2333979X-RAY DIFFRACTION82.03
1.74-1.770.30611150.22194104X-RAY DIFFRACTION84.79
1.77-1.810.28911410.21024189X-RAY DIFFRACTION87.35
1.81-1.860.23861460.20014348X-RAY DIFFRACTION89.13
1.86-1.90.25341430.18074322X-RAY DIFFRACTION90.49
1.9-1.950.23231540.15994635X-RAY DIFFRACTION95.38
1.95-2.010.22751470.1634598X-RAY DIFFRACTION96.01
2.01-2.080.21261530.1494696X-RAY DIFFRACTION96.96
2.08-2.150.20641630.14814682X-RAY DIFFRACTION97.33
2.15-2.240.19481580.14594685X-RAY DIFFRACTION97.86
2.24-2.340.20851620.14234761X-RAY DIFFRACTION98.24
2.34-2.460.19311610.15424719X-RAY DIFFRACTION98.59
2.46-2.620.18981610.15614817X-RAY DIFFRACTION99.72
2.62-2.820.20651570.17224806X-RAY DIFFRACTION99.68
2.82-3.10.24531550.16754786X-RAY DIFFRACTION99.06
3.1-3.550.18381560.15754719X-RAY DIFFRACTION98.09
3.55-4.470.15391570.13314831X-RAY DIFFRACTION99.84
4.47-37.390.16341520.14054720X-RAY DIFFRACTION98.07

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