PDB-7k05: Crystal structures and ribonuclease activity of the Flavivirus ho...

ID or keywords:

Entry

Database: PDB / ID: 7k05

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: 1.85 Å

Authors

Thapar, R. / Andrew, 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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Download

PDBx/mmCIF format	7k05.cif.gz	219.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7k05.ent.gz	146 KB	Display	PDB format
PDBx/mmJSON format	7k05.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k0/7k05 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/7k05	HTTPS FTP

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Related structure data

Related structure data	7lpyC 7lpzC 7lq0C 2xriS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7k07-2 7k07-1 7k05-2 3uyw-4 7k06-1 3uyw-2 4z9d-4 2gbz-d 4xin-d 3exv-d 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
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: ERI1 exoribonuclease 3

B: ERI1 exoribonuclease 3

hetero molecules

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

1

A: ERI1 exoribonuclease 3

hetero molecules

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

2

B: ERI1 exoribonuclease 3

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.579, 74.346, 96.513
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 / Fragment: exonuclease domain 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 / 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
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.1 Å³/Da / Density % sol: 41.31 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 30% MPEG 2K, 20% saturated KCl, 200 mM pH 8.4 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: 1.005 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.005 Å / Relative weight: 1
Reflection	Resolution: 1.85→48.3 Å / Num. obs: 69137 / % possible obs: 99.5 % / Redundancy: 9.8 % / B_iso Wilson estimate: 35.53 Å² / R_pim(I) all: 0.027 / R_rim(I) all: 0.088 / Net I/σ(I): 51.7
Reflection shell	Resolution: 1.85→1.88 Å / Num. unique obs: 3207 / CC_1/2: 0.844

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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: 1.85→37.25 Å / SU ML: 0.2249 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.4105

	R_factor	Num. reflection	% reflection
R_free	0.2117	3334	4.98 %
R_work	0.1715	-	-
obs	0.1734	67010	96.44 %

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å

Displacement parameters

B_iso mean: 50.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→37.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3222	0	56	176	3454

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3385
X-RAY DIFFRACTION	f_angle_d	1.2822	4598
X-RAY DIFFRACTION	f_chiral_restr	0.0768	492
X-RAY DIFFRACTION	f_plane_restr	0.0085	579
X-RAY DIFFRACTION	f_dihedral_angle_d	17.6093	1265

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 (%)
1.85-1.88	0.4053	111	0.2828	2257	X-RAY DIFFRACTION	82.02
1.88-1.9	0.2825	136	0.2559	2397	X-RAY DIFFRACTION	87.44
1.9-1.93	0.3023	131	0.2423	2462	X-RAY DIFFRACTION	90.6
1.93-1.97	0.2833	128	0.2307	2563	X-RAY DIFFRACTION	91.44
1.97-2	0.2699	130	0.2265	2522	X-RAY DIFFRACTION	92.92
2-2.04	0.2402	140	0.2191	2591	X-RAY DIFFRACTION	94.56
2.04-2.08	0.2352	137	0.2085	2632	X-RAY DIFFRACTION	95.22
2.08-2.12	0.2825	133	0.2054	2604	X-RAY DIFFRACTION	95.23
2.12-2.16	0.2336	147	0.2027	2649	X-RAY DIFFRACTION	96.18
2.16-2.21	0.2498	138	0.1815	2719	X-RAY DIFFRACTION	97.94
2.21-2.27	0.2592	138	0.1868	2704	X-RAY DIFFRACTION	98.58
2.27-2.33	0.2452	141	0.1923	2709	X-RAY DIFFRACTION	98.11
2.33-2.4	0.2355	145	0.1942	2721	X-RAY DIFFRACTION	99.07
2.4-2.48	0.2598	143	0.196	2738	X-RAY DIFFRACTION	99.45
2.48-2.57	0.2579	140	0.1983	2761	X-RAY DIFFRACTION	99.32
2.57-2.67	0.245	145	0.1884	2711	X-RAY DIFFRACTION	99.48
2.67-2.79	0.2683	145	0.1935	2750	X-RAY DIFFRACTION	99.83
2.79-2.94	0.2017	149	0.1906	2743	X-RAY DIFFRACTION	99.97
2.94-3.12	0.2356	148	0.1938	2764	X-RAY DIFFRACTION	99.93
3.12-3.36	0.2226	144	0.1732	2709	X-RAY DIFFRACTION	99.89
3.36-3.7	0.1812	143	0.1573	2754	X-RAY DIFFRACTION	99.79
3.7-4.23	0.1717	142	0.1416	2769	X-RAY DIFFRACTION	99.52
4.23-5.33	0.1728	140	0.1324	2716	X-RAY DIFFRACTION	98.72
5.33-37.25	0.1826	140	0.1578	2731	X-RAY DIFFRACTION	99.41

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	0.914606657442	-0.19471126647	0.0876493691063	0.412172422592	-0.430668081845	0.476970661262	-0.0269500926516	-0.158271955291	0.0445253594257	0.0566337056177	0.163860831026	0.118390688047	-0.118445141106	-0.0526739365104	4.87677913423E-5	0.267856156028	-0.000400651123734	0.00517356226938	0.296484789564	-0.0723606463598	0.305939923003	59.9776266672	28.6234596594	8.83453026601
2	1.22196585946	-0.070567241513	0.947551628753	1.05656131609	-0.600124800153	0.427218832922	-0.0375494063729	-0.100168291977	-0.203053757259	0.117681412636	0.00335648214097	0.17766318484	0.111495951267	-0.0190489150133	7.58726151134E-5	0.267411002594	-0.0275381480318	-0.0310111568616	0.342457640854	-0.0256471751131	0.336794488173	59.023573317	17.2786061985	2.25362874138
3	0.337693094101	-0.198309885432	-0.110843730596	0.468332036291	-0.0231344256454	0.104882807537	0.178072226773	0.192853544476	-0.599667637906	-0.139331888032	-0.153820204135	0.164371695698	0.357293766338	-0.0909333839573	-0.000341110154985	0.343155686118	-0.0245571578638	-0.0806480002491	0.371432332989	-0.0587210166522	0.432099113416	59.4037585373	4.34873300572	-4.57423743105
4	0.234555398015	0.0519375641106	-0.0681064433996	0.325688013718	-0.123021024449	0.0124856849209	0.0995526181895	0.240636279193	-0.146594332639	-0.212588239836	-0.239734290911	0.552867608208	-0.158167407839	-0.190696197614	-0.000165160381634	0.286145683189	0.0375535228049	-0.0391116755414	0.423649838306	6.07375455725E-5	0.334919054091	51.9025435704	23.2420270542	-7.00163353353
5	0.822197302968	0.496568637456	-0.507226278287	0.402654923273	0.290590312287	0.962052065648	0.170492128791	0.253284843031	0.259300497733	-0.0720776462483	-0.00159993248869	-0.248083658695	-0.154153906881	0.0911745525569	-3.28043713867E-5	0.275769260102	-0.00735644429385	0.0194103362396	0.379983502656	0.018820710269	0.322460741385	63.3953751707	25.7936173651	-4.14622529993
6	0.121224548609	-0.0406911745589	0.00593301762273	0.0332961340817	0.0442538349109	0.0871586964146	0.0794192066633	-0.212416007805	0.0935697674065	0.284566364124	0.0431547492251	-0.15614004615	0.251167201858	0.853719738374	4.51518853069E-5	0.343438908838	-0.0188980631787	-0.0322501541405	0.423378285282	-0.0604380216301	0.403591807453	70.8364642971	26.9046973606	11.8261384181
7	0.104865332307	0.0189495716934	-0.0934326968985	0.0174069839099	-0.0373207485482	0.047979774191	0.298301922787	-0.00305262063624	-0.172272729509	-0.0627185446997	0.00303591025562	0.113095555616	0.381710415802	0.340098328383	7.49486365583E-5	0.456663613839	0.0169576305914	-0.0558580938132	0.626137733003	-0.0571730365785	0.4466235124	72.6687235904	18.8363448893	16.6739728595
8	0.155367959612	0.0438190982233	0.0144536982855	0.0376567465457	0.0158909395198	0.0313874405967	0.113603967015	0.154997561823	-0.279584004694	0.566562825562	0.213183617069	-0.0603285336052	0.801318680765	0.286722543613	-0.000721502914514	0.548675261782	-0.0241630823937	-0.0465731935093	0.581193212988	0.0339927497728	0.453160307752	61.5687422123	12.7211909778	15.9892567239
9	0.16061056474	-0.197818744862	0.156944763113	0.116835872553	-0.146031043226	0.151770017216	-0.143507880973	-0.0780279473364	-0.181345900491	0.213280202174	0.200331786444	0.452776714423	0.263251239141	-0.238335620338	1.46905188161E-5	0.348996038284	0.0124965747683	-0.0213494836174	0.419464456386	-0.0153965919414	0.283907502268	60.3091921815	22.2068424398	15.4511581672
10	0.0443154884828	-0.0699830305467	0.0761294253044	0.0310409238214	-0.0529243517559	0.0318733609543	-0.206086971162	0.125523374023	0.490611127037	0.146986986015	0.209183312443	-0.626068476119	-0.204757332913	0.290023115948	0.000161422075636	0.378307104666	-0.0345576505038	-0.0123387125183	0.399369042069	-0.147992145787	0.562118163055	68.3710493417	33.1982432383	9.52901688384
11	2.55400636608	1.7480134641	-2.47807337978	2.53978526049	-2.68054415598	3.7729882002	0.37864672503	0.297312754471	0.489988704881	0.50233153929	0.298467342777	0.723674190325	-0.855143226094	-0.50340290149	0.725629711465	0.597878462367	0.0589729667631	0.173545118578	0.283460577185	0.0639001660124	0.453581953602	49.5211346489	49.3245182863	-12.517707738
12	1.45275242758	0.0933152299304	-1.45081763902	1.07952852419	-0.784395982098	1.60053064683	0.316673788244	-0.0309115520178	-0.0246578310653	0.414991075612	-0.27094529354	0.0564153680584	-0.390063002167	0.470204148426	0.0220487359234	0.544264411566	-0.114715744547	0.0317812179348	0.422417787835	0.0565352696761	0.378268092937	65.0627309886	51.3317434416	-18.3833831537

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 136 through 154 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 155 through 187 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 188 through 216 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 217 through 231 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 232 through 271 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 272 through 283 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 284 through 297 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 298 through 308 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 309 through 326 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 327 through 335 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 136 through 271 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 272 through 335 )

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