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- PDB-7lq0: Crystal structures and ribonuclease activity of the Flavivirus ho... -

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Entry
Database: PDB / ID: 7lq0
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 / ERI1 exoribonuclease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,0209
Polymers50,1362
Non-polymers8847
Water5,477304
1
A: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4644
Polymers25,0681
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5565
Polymers25,0681
Non-polymers4884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.529, 74.200, 96.487
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 136 through 181 or resid 183 through 285 or resid 287 through 503))
d_2ens_1(chain "B" and (resid 136 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_1METGLUA1 - 46
d_12ens_1THRCYSA50 - 152
d_13ens_1PROLYSA156 - 204
d_14ens_1AMPAMPB
d_15ens_1MGMGC
d_21ens_1METGLUE1 - 46
d_22ens_1THRCYSE48 - 150
d_23ens_1PROLYSE152 - 200
d_24ens_1AMPAMPF
d_25ens_1MGMGG

NCS oper: (Code: givenMatrix: (0.0195617615496, 0.117914462561, 0.992831061664), (0.211964313925, 0.96995921645, -0.119374402813), (-0.977081607189, 0.212779928432, -0.00601954725356)Vector: 47. ...NCS oper: (Code: given
Matrix: (0.0195617615496, 0.117914462561, 0.992831061664), (0.211964313925, 0.96995921645, -0.119374402813), (-0.977081607189, 0.212779928432, -0.00601954725356)
Vector: 47.0101958177, 17.4886004459, 41.6140294455)

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / 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.: 304 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 37.5% PEG 3350, 20% saturated KCl, 200 mM Imidazole / Malate buffer 8.0, 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: 1.6→37.23 Å / Num. obs: 368988 / % possible obs: 99.8 % / Redundancy: 6.59 % / Biso Wilson estimate: 29.33 Å2 / CC1/2: 1 / Net I/σ(I): 23.15
Reflection shellResolution: 1.6→1.7 Å / Num. unique obs: 60361 / CC1/2: 0.636

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Processing

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

2xri


Resolution: 1.6→37.23 Å / SU ML: 0.2156 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.1387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 3435 3.59 %
Rwork0.1623 92356 -
obs0.1636 95791 89.5 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.98 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 56 304 3582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01243385
X-RAY DIFFRACTIONf_angle_d1.1244598
X-RAY DIFFRACTIONf_chiral_restr0.0681492
X-RAY DIFFRACTIONf_plane_restr0.0073579
X-RAY DIFFRACTIONf_dihedral_angle_d16.64991265
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.526107960493 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.4181120.42842824X-RAY DIFFRACTION68.04
1.62-1.650.41281140.40012863X-RAY DIFFRACTION69.75
1.65-1.670.39841150.35373023X-RAY DIFFRACTION72.86
1.67-1.70.33781180.33183037X-RAY DIFFRACTION74.2
1.7-1.720.30531130.31563205X-RAY DIFFRACTION77.27
1.72-1.750.36511200.28533252X-RAY DIFFRACTION79.15
1.75-1.790.28651260.27043360X-RAY DIFFRACTION81.64
1.79-1.820.29521290.24853464X-RAY DIFFRACTION83.06
1.82-1.860.31481200.23463416X-RAY DIFFRACTION82.71
1.86-1.90.25141330.21233574X-RAY DIFFRACTION86.88
1.9-1.940.28161480.19023721X-RAY DIFFRACTION91.16
1.94-1.990.26571430.18453846X-RAY DIFFRACTION93.33
1.99-2.040.21911390.17073959X-RAY DIFFRACTION95.13
2.04-2.10.22521510.1683941X-RAY DIFFRACTION95.83
2.1-2.170.23141520.16614008X-RAY DIFFRACTION96.43
2.17-2.250.20421450.14814064X-RAY DIFFRACTION97.95
2.25-2.340.22011480.16183990X-RAY DIFFRACTION97.55
2.34-2.450.20741480.15564029X-RAY DIFFRACTION97.68
2.45-2.580.21721480.16514079X-RAY DIFFRACTION99.41
2.58-2.740.2161540.1614121X-RAY DIFFRACTION99.67
2.74-2.950.20511530.16634140X-RAY DIFFRACTION99.88
2.95-3.240.19681520.16964123X-RAY DIFFRACTION99.91
3.24-3.710.1871470.14694088X-RAY DIFFRACTION98.95
3.71-4.680.14031550.12714123X-RAY DIFFRACTION99.91
4.68-37.230.17691520.14524106X-RAY DIFFRACTION99.6

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