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

ID or keywords:

Entry

Database: PDB / ID: 7k06

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-prime - 5-prime exoribonucleases

Components

ERI1 exoribonuclease 3

Keywords

HYDROLASE / 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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Thapar, R. / Arvai, A.S. / Tainer, J.A.

Funding support

1items

Citation

Journal: 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

Deposition	Sep 3, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7k06.cif.gz	224.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7k06_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7k06_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7k06_validation.xml.gz	18.4 KB	Display
Data in CIF	7k06_validation.cif.gz	26.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k0/7k06 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/7k06	HTTPS FTP

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Related structure data

Related structure data	7k07C 2xriS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7k05-2 2vlb-2 4kbr-4 2vpv-d 4nt1-1 2nu0-d 7k05-1 1iad-d 7k07-2 5ux1-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ERI1 exoribonuclease 3

B: ERI1 exoribonuclease 3

hetero molecules

50.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ERI1 exoribonuclease 3

hetero molecules

defined by author
25.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ERI1 exoribonuclease 3

hetero molecules

defined by author
25.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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 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 Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.26 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97934 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.95→48.4 Å / Num. obs: 31492 / % possible obs: 99.8 % / Redundancy: 12.5 % / B_iso Wilson estimate: 16.23 Å² / R_pim(I) all: 0.012 / R_rim(I) all: 0.044 / Net I/σ(I): 58.1
Reflection shell	Resolution: 1.95→1.98 Å / Num. unique obs: 1497 / CC_1/2: 0.795

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2226	1473	4.98 %
R_work	0.1814	-	-
obs	0.1836	29563	94.23 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å

Displacement parameters

B_iso mean: 24.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→40.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3222	0	44	224	3490

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0031	3373
X-RAY DIFFRACTION	f_angle_d	0.6084	4580
X-RAY DIFFRACTION	f_chiral_restr	0.043	492
X-RAY DIFFRACTION	f_plane_restr	0.0042	580
X-RAY DIFFRACTION	f_dihedral_angle_d	15.2788	1247

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-2.01	0.3077	80	0.243	1520	X-RAY DIFFRACTION	56.98
2.01-2.09	0.3114	122	0.2211	2433	X-RAY DIFFRACTION	91.71
2.09-2.17	0.2825	137	0.2031	2554	X-RAY DIFFRACTION	95.36
2.17-2.27	0.2358	137	0.1904	2593	X-RAY DIFFRACTION	97.12
2.27-2.39	0.2709	135	0.1973	2603	X-RAY DIFFRACTION	97.23
2.39-2.54	0.2273	140	0.2013	2670	X-RAY DIFFRACTION	98.98
2.54-2.73	0.2741	138	0.2015	2652	X-RAY DIFFRACTION	99.01
2.73-3.01	0.2492	143	0.2007	2704	X-RAY DIFFRACTION	99.62
3.01-3.44	0.2441	144	0.1913	2729	X-RAY DIFFRACTION	99.97
3.44-4.34	0.1618	145	0.1484	2760	X-RAY DIFFRACTION	99.76
4.34-40.55	0.1549	152	0.1441	2872	X-RAY DIFFRACTION	99.8

Refinement TLS params.

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

ID	L11 (°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)
1	1.49148477884	-0.34171410163	-0.0653306398075	1.22567738477	0.0668458862445	0.891356946166	0.0937405189322	0.0283410642597	0.000798612347644	0.00508600014387	0.040224741834	-0.028714175556	-0.0314325770474	-0.0304280856228	-0.0470186990589	0.0125480461111	-0.0221695748519	-0.037759265999	0.0958560374429	0.00229027185115	0.0853703194726	59.4249337471	19.5945723612	-1.00092123584
2	1.86169917487	0.290851973661	0.835798923544	1.85297964297	-0.185141957035	2.16788311346	0.0724152682295	-0.346438025262	-0.0213975705887	0.272355044018	0.0640090352074	-0.173396862799	0.0155838291498	0.0248183722941	-0.0795525255002	0.0786397698459	0.00224965542657	-0.0322881512505	0.197649890017	-0.0382324426237	0.115608390505	65.9863315549	22.2199010752	14.3081214988
3	1.50053328804	0.631285276257	0.686323975776	2.17171150339	0.844930108689	0.706921615753	0.0136274281977	-0.0886845161399	0.4025299057	0.197562988437	0.127412368896	-0.151524367597	-0.449790335462	0.33410788739	-0.0547062831814	0.6181093947	-0.152866688756	0.118717624161	0.259239855209	-0.072957315436	0.316648491184	60.1439973463	57.075784538	-10.9630257657
4	3.10405730826	1.20508187474	0.105014923598	2.62025261108	0.107462272279	1.66950165616	-0.0305775419328	0.244999012144	0.302076617393	0.111537552053	0.23563566196	0.223560141592	-0.365456286605	0.176049197023	-0.129708266936	0.344144381736	-0.0584102007079	0.0892928472546	0.15013139221	0.028776462297	0.17203057734	52.1815648743	46.561986257	-12.5786055549
5	3.33726357145	1.12840549586	-0.801326286942	3.07904381689	-1.24773786723	3.16990816698	-0.0699927109723	0.568454270705	0.158070388009	-0.288388309574	0.285337424269	0.278766722566	0.0270073744307	-0.58583617524	-0.200245565723	0.147760979257	-0.0732848075051	0.0329512567754	0.282424163103	0.0737809906571	0.178909220738	44.0772884484	34.9637938139	-15.5855868123
6	1.10590898427	-0.0775509445925	0.340292882271	1.44568237293	2.06067478748	4.06248178463	0.0843340645057	-0.236871233528	0.12631592778	0.188893716821	-0.0440872778605	0.166751324959	-0.192622585986	-0.259274027346	0.0334947526664	0.610625479722	0.0766105729148	0.309935565809	0.256380308139	0.0407622448034	0.430278136299	43.8181263684	51.904038355	-4.15530032363
7	0.493679345698	0.254795441998	-0.22410800489	1.44533362278	-0.3872802682	0.852930241735	0.0673174430582	-0.0536674581796	0.285840055769	0.452813099499	0.19170209906	0.548200512232	-0.341971544053	-0.267308779968	-0.259020953037	0.511570795528	0.0555951272575	0.179784790084	0.226219607643	0.139979158456	0.40965268754	51.2773345048	56.7686088288	-16.676723441
8	3.18133358723	-1.38689110138	-1.31523149488	4.02128481071	-3.9109107847	7.0280969104	-0.0190866956944	0.252640519219	0.0352580526576	-0.153522687145	0.0182307434339	0.0447146307087	-0.0211800459613	0.127119148049	-0.00511236909212	0.182150185374	-0.063503127536	0.0223967719303	0.19255506659	0.0379608985467	0.112037678545	67.2025835474	48.0329466004	-24.4820604929
9	4.03254965193	1.43604827893	-1.21798244971	4.64822980499	-0.989545329527	2.36358988232	-0.0460297661595	-0.117464066957	-0.00721380739584	0.197957478239	-0.077818287971	-0.264653289742	-0.368332492058	0.610980172359	0.102721735455	0.294661307183	-0.0973637959766	0.0169696753525	0.223623813805	0.0298609311704	0.101021101895	64.9263213782	45.8913697097	-13.7301841337
10	6.92396516366	1.79712639896	0.927011954677	2.89540719943	-0.0529115439796	0.395230039632	-0.0167123310433	0.298469291732	0.69062035341	-0.110850676851	0.0404258728983	0.0516176113163	-0.328929293774	0.112019838583	0.0130557867416	0.664746801014	-0.10046177391	0.153431265824	0.236882832311	0.0568728790715	0.41155530087	63.1844445743	62.367919039	-17.9462160981

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 136 through 271 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 272 through 335 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 136 through 154 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 155 through 187 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 188 through 216 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 217 through 231 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 232 through 283 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 284 through 298 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 299 through 325 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 326 through 335 )

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