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- PDB-7k06: Crystal structures and ribonuclease activity of the Flavivirus ho... -

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Database: PDB / ID: 7k06
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
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
CYTIDINE-5'-MONOPHOSPHATE / ERI1 exoribonuclease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
AuthorsThapar, R. / Arvai, A.S. / Tainer, J.A.
Funding support1items
OrganizationGrant numberCountry
Robert A. Welch Foundation
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.
DepositionSep 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release

Structure visualization

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

Theoretical massNumber of molelcules
Total (without water)50,8316
A: ERI1 exoribonuclease 3
hetero molecules

Theoretical massNumber of molelcules
Total (without water)25,4163
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
B: ERI1 exoribonuclease 3
hetero molecules

Theoretical massNumber of molelcules
Total (without water)25,4163
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.417, 74.234, 96.836
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


#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-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate

Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 25% MPEG 2K, 15% saturated KCl, 200 mM pH 7.8 imidazole / malate

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.95→48.4 Å / Num. obs: 31492 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 16.23 Å2 / Rpim(I) all: 0.012 / Rrim(I) all: 0.044 / Net I/σ(I): 58.1
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 1497 / CC1/2: 0.795


HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XRI
Resolution: 1.95→40.55 Å / SU ML: 0.217 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.5264
RfactorNum. reflection% reflection
Rfree0.2226 1473 4.98 %
Rwork0.1814 --
obs0.1836 29563 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 24.89 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 44 224 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313373
X-RAY DIFFRACTIONf_angle_d0.60844580
X-RAY DIFFRACTIONf_chiral_restr0.043492
X-RAY DIFFRACTIONf_plane_restr0.0042580
X-RAY DIFFRACTIONf_dihedral_angle_d15.27881247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.3077800.2431520X-RAY DIFFRACTION56.98
2.01-2.090.31141220.22112433X-RAY DIFFRACTION91.71
2.09-2.170.28251370.20312554X-RAY DIFFRACTION95.36
2.17-2.270.23581370.19042593X-RAY DIFFRACTION97.12
2.27-2.390.27091350.19732603X-RAY DIFFRACTION97.23
2.39-2.540.22731400.20132670X-RAY DIFFRACTION98.98
2.54-2.730.27411380.20152652X-RAY DIFFRACTION99.01
2.73-3.010.24921430.20072704X-RAY DIFFRACTION99.62
3.01-3.440.24411440.19132729X-RAY DIFFRACTION99.97
3.44-4.340.16181450.14842760X-RAY DIFFRACTION99.76
4.34-40.550.15491520.14412872X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 136 through 271 )
2X-RAY DIFFRACTION2chain 'A' and (resid 272 through 335 )
3X-RAY DIFFRACTION3chain 'B' and (resid 136 through 154 )
4X-RAY DIFFRACTION4chain 'B' and (resid 155 through 187 )
5X-RAY DIFFRACTION5chain 'B' and (resid 188 through 216 )
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 231 )
7X-RAY DIFFRACTION7chain 'B' and (resid 232 through 283 )
8X-RAY DIFFRACTION8chain 'B' and (resid 284 through 298 )
9X-RAY DIFFRACTION9chain 'B' and (resid 299 through 325 )
10X-RAY DIFFRACTION10chain 'B' and (resid 326 through 335 )

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