PDB-8wu3: Crystal structure of RNA-dependent RNA polymerases from Alongshan...

ID or keywords:

Entry

Database: PDB / ID: 8wu3

Title

Crystal structure of RNA-dependent RNA polymerases from Alongshan virus

Components

RNA polymerase

Keywords

VIRAL PROTEIN / RNA polymerase

Biological species

Alongshan virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Liu, Z.Y. / Han, P. / Peng, Q. / Qi, J.X.

Funding support

China, 1items

Citation

Journal: HLIFE / Year: 2024
Title: Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus
Authors: Liu, Z. / Peng, Q. / Han, P. / Kuai, L. / Qi, J. / Shi, Y.

History

Deposition	Oct 20, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 7, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	Group: Database references / Source and taxonomy / Structure summary Category: citation / entity / entity_src_gen Item: _citation.country / _entity.details ..._citation.country / _entity.details / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8wu3.cif.gz	577.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8wu3.ent.gz	407.1 KB	Display	PDB format
PDBx/mmJSON format	8wu3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8wu3_validation.pdf.gz	449.3 KB	Display	wwPDB validaton report
Full document	8wu3_full_validation.pdf.gz	465 KB	Display
Data in XML	8wu3_validation.xml.gz	41.3 KB	Display
Data in CIF	8wu3_validation.cif.gz	55.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wu/8wu3 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/8wu3	HTTPS FTP

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Related structure data

Related structure data	8wu2C C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#40 - Apr 2003 RNA Polymerase similarity (1)

Deposited unit

A: RNA polymerase

B: RNA polymerase

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	75.351, 93.358, 101.686
Angle α, β, γ (deg.)	90.000, 98.090, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	RNA polymerase Mass: 71182.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GeneBank: MH158415.1 / Source: (gene. exp.) Alongshan virus / Production host: Escherichia coli (E. coli)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.01 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.1→48.19 Å / Num. obs: 21699 / % possible obs: 93.5 % / Redundancy: 5 % / B_iso Wilson estimate: 71.06 Å² / R_merge(I) obs: 0.17 / Net I/σ(I): 9
Reflection shell	Resolution: 3.1→3.31 Å / R_merge(I) obs: 1.024 / Num. unique obs: 1503

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→48.19 Å / SU ML: 0.4412 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.1352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2753	1999	9.25 %
R_work	0.2566	19615	-
obs	0.2583	21614	93.15 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 88.83 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→48.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9503	0	0	0	9503

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0036	9704
X-RAY DIFFRACTION	f_angle_d	0.6969	13085
X-RAY DIFFRACTION	f_chiral_restr	0.0436	1390
X-RAY DIFFRACTION	f_plane_restr	0.0104	1678
X-RAY DIFFRACTION	f_dihedral_angle_d	4.7818	1329

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 (%)
3.2-3.28	0.3575	96	0.3515	946	X-RAY DIFFRACTION	62.1
3.28-3.37	0.3451	111	0.3238	1085	X-RAY DIFFRACTION	74.42
3.37-3.47	0.3297	125	0.3261	1228	X-RAY DIFFRACTION	82.55
3.47-3.58	0.3484	141	0.313	1383	X-RAY DIFFRACTION	91.92
3.58-3.71	0.3269	148	0.2966	1452	X-RAY DIFFRACTION	97.56
3.71-3.86	0.3475	151	0.2964	1475	X-RAY DIFFRACTION	98.49
3.86-4.03	0.2944	152	0.2846	1494	X-RAY DIFFRACTION	99.76
4.03-4.24	0.2933	152	0.2475	1493	X-RAY DIFFRACTION	99.58
4.24-4.51	0.2675	154	0.2432	1504	X-RAY DIFFRACTION	99.76
4.51-4.86	0.2462	150	0.2316	1480	X-RAY DIFFRACTION	99.39
4.86-5.34	0.2523	153	0.2369	1512	X-RAY DIFFRACTION	99.58
5.35-6.12	0.277	153	0.2566	1501	X-RAY DIFFRACTION	99.64
6.12-7.7	0.2445	155	0.257	1524	X-RAY DIFFRACTION	100
7.7-48.19	0.2076	158	0.1936	1538	X-RAY DIFFRACTION	98.95

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	1.70572309163	-1.01836123934	2.69073796843	0.541445149131	-0.295148534074	2.65843211769	-0.260401837678	-0.369256583639	0.44611194062	0.0506837080458	0.0333190321778	0.233353503548	-0.522074517892	-1.2086503451	0.2182638756	0.827254888708	0.15510017767	0.0417784244813	1.31571383671	0.063449058022	0.650607745362	14.9176548554	76.6316599204	2.40539878244
2	3.34947582221	-1.25257590677	1.20954794848	2.28529712198	-1.09376824729	3.61280818212	0.0848541151756	-0.385034770779	-0.0621178791615	0.180544943921	0.152436659169	0.591220548144	0.270274084738	-0.699763536196	-0.23638804033	0.418367257584	-0.112593635081	-0.00499143205951	0.647151599399	0.0587646652691	0.405861055736	16.6398920644	63.797082293	-6.55881719664
3	2.59996828661	-0.701370744499	1.18356873807	4.97655955008	1.87505226389	2.82616436513	0.0117823181567	-1.2116701267	-0.0626065611569	1.2696515864	0.011631661175	0.606676863951	0.347490043612	-1.95844259367	-0.0044994253992	0.829930135743	-0.073991226256	0.0138419359233	1.84662718427	0.198417767419	0.732052493435	8.67605402418	63.2100917675	13.4316016392
4	4.62325622791	-2.67927242548	2.41945552697	1.73957170527	-0.930663383608	4.09155483912	0.48695645566	-0.632947621595	-0.891460343591	-0.145757444077	0.214769779889	0.535669090722	0.414632730825	-0.581569212824	-0.674650565252	0.629069637575	-0.204218046584	-0.066403346227	0.480814022184	0.117239399734	0.501731079568	22.8748759438	53.5641405991	-3.87266273963
5	2.25375328152	-0.784555395847	1.82790687452	4.84158882995	-1.85189045658	4.15556265139	-0.363103725066	-0.358516411897	0.0303108921629	0.411661979408	1.0339362517	0.855347530857	-0.0942220949873	-1.56079083951	-0.650628130255	0.504700452733	0.129798750327	0.0127084742036	1.51674971677	0.0967091387299	0.7819217193	6.88328519387	69.690192507	2.0177157813
6	3.77307581745	-0.835456921324	2.2332538346	1.88291995207	-2.38071606205	5.19825570015	0.256716644212	-0.0391395727865	-0.361745747609	-0.441282008529	0.17773199479	0.271946891226	0.628511219826	-0.303506748515	-0.378511272741	0.69447427452	-0.0825231868719	-0.0701894526883	0.193903175176	0.0706575291587	0.526833667217	29.8101255962	55.1089792213	-7.44355369377
7	2.39442186634	-0.174051571689	-0.0958596461477	7.67618537598	1.95192086084	6.71697183748	0.0953479482938	-0.0313579290039	0.248289454298	0.409386924835	0.00625968586141	0.0943559356332	-0.22492310412	0.0797454435901	-0.102428462841	0.566700518524	-0.0339320780025	0.0682606889308	0.191079071817	0.0536031265549	0.481133571613	43.4968936046	59.7810615508	18.6993356351
8	2.0529382995	0.850542211287	-2.07624988263	-0.317204499582	0.0583455677905	3.25651428802	-0.151107095221	1.08331245876	-0.182508768523	-0.551695494809	0.400052331872	0.266012965192	0.782832170562	-1.7124292916	-0.225402737728	1.29752798143	-0.319630611733	-0.221861760893	1.30283101731	0.186647838312	0.966876331152	8.86862308001	26.7448004244	39.1879244253
9	4.55457500816	0.99720138083	-3.92512031012	1.387047056	-2.68619902942	5.27016554812	-0.113349746409	1.19526893559	0.496899666511	-0.270744515426	0.755056296643	0.516184987758	0.286359570479	-1.43219513258	-0.487799358759	0.832088271276	-0.0659735858556	-0.0850053788537	0.657236189943	0.189174623883	0.573582987552	15.827580809	37.0362879973	47.4601037026
10	2.61046976887	-1.28466751605	-1.11249578384	5.64668172571	2.25356835868	6.79859342568	0.0738446600541	-0.10012974156	0.148114917867	0.0474749125938	0.0285168420391	-0.0290971917845	0.00238056281337	0.268700534092	-0.0961656304417	0.639605547638	-0.0395104405491	-0.00884357217959	0.192441579392	0.046166978057	0.444462283473	42.6021477576	36.7562423036	34.5968370449

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 11 through 89 )	A	A	11 - 89	1 - 79
2	2	chain 'A' and (resid 90 through 141 )	A	A	90 - 141	80 - 126
3	3	chain 'A' and (resid 142 through 251 )	A	A	142 - 251	127 - 222
4	4	chain 'A' and (resid 252 through 306 )	A	A	252 - 306	223 - 277
5	5	chain 'A' and (resid 307 through 355 )	A	A	307 - 355	278 - 326
6	6	chain 'A' and (resid 356 through 492 )	A	A	356 - 492	327 - 460
7	7	chain 'A' and (resid 493 through 621 )	A	A	493 - 621	461 - 589
8	8	chain 'B' and (resid 11 through 197 )	B	B	11 - 197	1 - 185
9	9	chain 'B' and (resid 198 through 509 )	B	B	198 - 509	186 - 480
10	10	chain 'B' and (resid 510 through 621 )	B	B	510 - 621	481 - 592

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