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

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Basic information

Entry
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
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
CYTIDINE-5'-MONOPHOSPHATE / ERI1 exoribonuclease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
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.
History
DepositionSep 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)50,8316
Polymers50,1362
Non-polymers6954
Water4,035224
1
A: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4163
Polymers25,0681
Non-polymers3482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ERI1 exoribonuclease 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4163
Polymers25,0681
Non-polymers3482
Water181
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

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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-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

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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: 41.26 %
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

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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

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XRI

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.49148477884-0.34171410163-0.06533063980751.225677384770.06684588624450.8913569461660.09374051893220.02834106425970.0007986123476440.005086000143870.040224741834-0.028714175556-0.0314325770474-0.0304280856228-0.04701869905890.0125480461111-0.0221695748519-0.0377592659990.09585603744290.002290271851150.085370319472659.424933747119.5945723612-1.00092123584
21.861699174870.2908519736610.8357989235441.85297964297-0.1851419570352.167883113460.0724152682295-0.346438025262-0.02139757058870.2723550440180.0640090352074-0.1733968627990.01558382914980.0248183722941-0.07955252550020.07863976984590.00224965542657-0.03228815125050.197649890017-0.03823244262370.11560839050565.986331554922.219901075214.3081214988
31.500533288040.6312852762570.6863239757762.171711503390.8449301086890.7069216157530.0136274281977-0.08868451613990.40252990570.1975629884370.127412368896-0.151524367597-0.4497903354620.33410788739-0.05470628318140.6181093947-0.1528666887560.1187176241610.259239855209-0.0729573154360.31664849118460.143997346357.075784538-10.9630257657
43.104057308261.205081874740.1050149235982.620252611080.1074622722791.66950165616-0.03057754193280.2449990121440.3020766173930.1115375520530.235635661960.223560141592-0.3654562866050.176049197023-0.1297082669360.344144381736-0.05841020070790.08929284725460.150131392210.0287764622970.1720305773452.181564874346.561986257-12.5786055549
53.337263571451.12840549586-0.8013262869423.07904381689-1.247737867233.16990816698-0.06999271097230.5684542707050.158070388009-0.2883883095740.2853374242690.2787667225660.0270073744307-0.58583617524-0.2002455657230.147760979257-0.07328480750510.03295125677540.2824241631030.07378099065710.17890922073844.077288448434.9637938139-15.5855868123
61.10590898427-0.07755094459250.3402928822711.445682372932.060674787484.062481784630.0843340645057-0.2368712335280.126315927780.188893716821-0.04408727786050.166751324959-0.192622585986-0.2592740273460.03349475266640.6106254797220.07661057291480.3099355658090.2563803081390.04076224480340.43027813629943.818126368451.904038355-4.15530032363
70.4936793456980.254795441998-0.224108004891.44533362278-0.38728026820.8529302417350.0673174430582-0.05366745817960.2858400557690.4528130994990.191702099060.548200512232-0.341971544053-0.267308779968-0.2590209530370.5115707955280.05559512725750.1797847900840.2262196076430.1399791584560.4096526875451.277334504856.7686088288-16.676723441
83.18133358723-1.38689110138-1.315231494884.02128481071-3.91091078477.0280969104-0.01908669569440.2526405192190.0352580526576-0.1535226871450.01823074343390.0447146307087-0.02118004596130.127119148049-0.005112369092120.182150185374-0.0635031275360.02239677193030.192555066590.03796089854670.11203767854567.202583547448.0329466004-24.4820604929
94.032549651931.43604827893-1.217982449714.64822980499-0.9895453295272.36358988232-0.0460297661595-0.117464066957-0.007213807395840.197957478239-0.077818287971-0.264653289742-0.3683324920580.6109801723590.1027217354550.294661307183-0.09736379597660.01696967535250.2236238138050.02986093117040.10102110189564.926321378245.8913697097-13.7301841337
106.923965163661.797126398960.9270119546772.89540719943-0.05291154397960.395230039632-0.01671233104330.2984692917320.69062035341-0.1108506768510.04042587289830.0516176113163-0.3289292937740.1120198385830.01305578674160.664746801014-0.100461773910.1534312658240.2368828323110.05687287907150.4115553008763.184444574362.367919039-17.9462160981
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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