PDB-6jim: Viral helicase protein

ID or keywords:

Entry

Database: PDB / ID: 6jim

Title

Viral helicase protein

Components

RNA (5'-R(P*UP*UP*UP*UP*UP)-3')
helicase

Keywords

VIRAL PROTEIN/RNA /

helicase /

VIRAL PROTEIN-RNA complex

Function / homology

Function and homology information

polynucleotide 5'-phosphatase /

: /

: / host cell filopodium /

ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity /

polynucleotide 5'-phosphatase activity /

polynucleotide adenylyltransferase / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping ...
Similarity search - Function

Biological species

Chikungunya virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Law, Y.S.

Funding support

Singapore, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase.
Authors: Law, Y.S. / Utt, A. / Tan, Y.B. / Zheng, J. / Wang, S. / Chen, M.W. / Griffin, P.R. / Merits, A. / Luo, D.

History

Deposition	Feb 22, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2	May 1, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	May 22, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4	Mar 27, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6jim.cif.gz	392.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6jim.ent.gz	318.9 KB	Display	PDB format
PDBx/mmJSON format	6jim.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/ji/6jim ftp://data.pdbj.org/pub/pdb/validation_reports/ji/6jim	HTTPS FTP

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Related structure data

Similar structure data	3pw7-1 3t5j-d 2jeg-d 4rzr-1 6go6-d 2of7-1 1ukc-1 3uxp-1 2r8g-d 2w9a-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	#106 - Oct 2008 Poly(A) Polymerase similarity (1)

Deposited unit

A: helicase

B: helicase

C: RNA (5'-R(P*UP*UP*UP*UP*UP)-3')

D: RNA (5'-R(P*UP*UP*UP*UP*UP)-3')

hetero molecules

111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: helicase

C: RNA (5'-R(P*UP*UP*UP*UP*UP)-3')

hetero molecules

defined by author&software
Evidence: gel filtration
55.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: helicase

D: RNA (5'-R(P*UP*UP*UP*UP*UP)-3')

hetero molecules

defined by author&software
55.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.888, 53.905, 100.718
Angle α, β, γ (deg.)	96.93, 94.07, 97.04
Int Tables number	1
Space group name H-M	P1

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein	helicase / Mass: 51910.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Plasmid: chikungunya virus / Cell line (production host): Rosetta / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A076V769*PLUS
#2: RNA chain	RNA (5'-R(PUPUPUPUPUP)-3') Mass: 2450.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source*: (synth.) Chikungunya virus

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Non-polymers , 7 types, 387 molecules

#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-AL / ALUMINUM ION / Aluminium Mass: 26.982 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Al
#6: Chemical	ChemComp-F / FLUORIDE ION / Fluoride Mass: 18.998 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: F
#7: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H₂O

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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: 53.05 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion / Details: 100 mM HEPES pH 7.5, 20 % PEG 8000

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9762 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 13, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2→35.324 Å / Num. obs: 73699 / % possible obs: 97.7 % / Redundancy: 4 % / CC_1/2: 0.995 / R_sym value: 0.0469 / Net I/σ(I): 1
Reflection shell	Resolution: 2→2.07 Å / Num. measured obs: 29255 / Num. unique obs: 7327 / CC_1/2: 0.344 / R_sym value: 0.805

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→35.32 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.15

	R_factor	Num. reflection	% reflection
R_free	0.215	3671	5 %
R_work	0.177	-	-
obs	0.179	73427	97.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2→35.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7026	296	167	352	7841

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7654
X-RAY DIFFRACTION	f_angle_d	0.895	10444
X-RAY DIFFRACTION	f_dihedral_angle_d	7.794	6230
X-RAY DIFFRACTION	f_chiral_restr	0.053	1210
X-RAY DIFFRACTION	f_plane_restr	0.004	1273

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 (%)
2-2.0263	0.3463	154	0.3093	2630	X-RAY DIFFRACTION	97
2.0263-2.0541	0.3421	148	0.2982	2683	X-RAY DIFFRACTION	97
2.0541-2.0834	0.3265	162	0.2936	2638	X-RAY DIFFRACTION	96
2.0834-2.1145	0.3494	129	0.2723	2621	X-RAY DIFFRACTION	97
2.1145-2.1475	0.3015	131	0.2662	2739	X-RAY DIFFRACTION	97
2.1475-2.1828	0.2699	122	0.2554	2668	X-RAY DIFFRACTION	97
2.1828-2.2204	0.2866	149	0.2329	2654	X-RAY DIFFRACTION	97
2.2204-2.2608	0.2866	141	0.2188	2692	X-RAY DIFFRACTION	97
2.2608-2.3042	0.2272	147	0.2213	2672	X-RAY DIFFRACTION	97
2.3042-2.3513	0.2391	146	0.2079	2689	X-RAY DIFFRACTION	98
2.3513-2.4024	0.2552	143	0.2082	2615	X-RAY DIFFRACTION	98
2.4024-2.4582	0.2578	139	0.2075	2755	X-RAY DIFFRACTION	98
2.4582-2.5197	0.2525	129	0.1945	2638	X-RAY DIFFRACTION	98
2.5197-2.5878	0.2427	170	0.196	2668	X-RAY DIFFRACTION	98
2.5878-2.6639	0.2047	131	0.1852	2694	X-RAY DIFFRACTION	98
2.6639-2.7499	0.2231	146	0.1784	2683	X-RAY DIFFRACTION	98
2.7499-2.8481	0.2416	131	0.1847	2767	X-RAY DIFFRACTION	98
2.8481-2.9621	0.2131	105	0.1809	2691	X-RAY DIFFRACTION	98
2.9621-3.0968	0.2204	133	0.174	2725	X-RAY DIFFRACTION	98
3.0968-3.26	0.2194	149	0.1645	2685	X-RAY DIFFRACTION	98
3.26-3.4641	0.2203	171	0.1658	2676	X-RAY DIFFRACTION	98
3.4641-3.7313	0.1772	135	0.1543	2687	X-RAY DIFFRACTION	98
3.7313-4.1063	0.1634	142	0.139	2702	X-RAY DIFFRACTION	98
4.1063-4.6993	0.1665	139	0.1402	2697	X-RAY DIFFRACTION	98
4.6993-5.9161	0.1967	174	0.1664	2681	X-RAY DIFFRACTION	98
5.9161-35.3	0.2116	105	0.1693	2706	X-RAY DIFFRACTION	97

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	0.9371	0.3156	-0.0727	0.7478	-0.2831	0.5447	-0.0536	0.364	0.39	-0.6824	0.0882	0.3433	-0.0503	-0.3516	-0.063	0.4656	0.0243	-0.0005	0.4527	0.1205	0.3367	19.6968	2.0186	36.5305
2	1.0235	0.0409	-0.8645	0.8302	-0.4175	0.9282	-0.4094	0.4172	-0.2214	-0.5771	0.4056	-0.1662	0.0922	-0.1315	0.0002	0.4052	-0.1	0.0325	0.4879	-0.0714	0.3169	20.2745	-22.5894	35.3911
3	0.1948	0.1006	-0.0083	1.0218	0.1049	1.1523	0.0625	-0.0864	-0.0532	0.1772	-0.0153	0.0199	0.0892	-0.1938	0.0002	0.2219	-0.0217	0.0133	0.3431	-0.0272	0.2607	27.328	-13.131	60.5772
4	0.3642	-0.1419	0.0233	1.0121	-0.2784	0.8531	0.0614	-0.0009	0.1342	-0.0683	0.0093	-0.1591	-0.122	-0.002	-0	0.2396	-0.0068	0.015	0.3042	-0.0217	0.3039	34.3611	-6.5657	54.2689
5	1.5542	-0.5931	-0.6594	1.2526	0.4301	1.2149	-0.0213	0.0249	-0.1604	0.0728	0.0226	-0.2704	0.0673	0.1872	-0.0167	0.1892	0.0033	0.0218	0.3212	-0.0278	0.383	49.3837	-22.2385	53.7198
6	0.6432	-0.2061	-0.3017	0.1805	-0.1142	0.368	0.1288	-0.3647	0.0658	0.5893	0.1061	0.3299	-0.6318	-0.2814	0.0252	0.6804	0.1205	0.1336	0.4676	0.0749	0.3403	24.7196	13.443	16.4961
7	1.0514	-0.2537	-0.0477	0.8432	-0.095	0.6284	0.163	-0.0845	0.053	0.5032	-0.0343	-0.1398	-0.141	0.0321	0.0419	0.5899	-0.0311	-0.1123	0.3106	0.037	0.277	48.7431	15.6401	17.1412
8	0.4647	-0.0361	0.1987	0.3957	-0.0325	1.1495	-0.0319	0.187	0.0082	0.0455	0.0893	-0.1211	-0.242	-0.0245	-0.0012	0.3669	-0.0071	-0.0167	0.2589	0.0101	0.2671	41.3676	7.318	-6.5134
9	0.6187	-0.3506	-0.6564	0.1958	0.3039	0.7502	-0.0353	0.0527	-0.1968	0.0689	0.0997	0.0824	0.1103	-0.1685	0.0003	0.3395	0.002	-0.0064	0.2814	0.0265	0.3104	34.7166	-0.4949	-1.5091
10	1.3916	-0.2213	0.2443	1.4603	-0.7244	1.5442	0.0185	-0.0017	-0.2528	0.0017	-0.063	-0.1959	0.2406	0.1221	-0	0.3543	0.0182	0.0001	0.2332	0.0211	0.3558	52.1076	-13.5264	-0.8764
11	0.1451	0.0998	-0.0967	0.2283	-0.1993	0.1184	-0.1591	0.2109	0.1569	0.1548	0.3718	-0.5855	1.0698	0.0297	0.0001	0.4331	0.0102	-0.0498	0.6737	-0.0782	0.5329	30.1802	-23.2147	45.9552
12	0.1516	0.1367	-0.0624	0.1322	-0.0874	0.0459	0.1971	0.0555	-0.1997	0.2523	0.0032	-0.1785	-0.0868	0.8004	0.0001	0.682	0.0282	-0.0875	0.4806	-0.0642	0.5001	50.7297	5.4045	6.842

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 78 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 79 THROUGH 160 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 161 THROUGH 247 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 248 THROUGH 314 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 315 THROUGH 463 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 1 THROUGH 78 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 79 THROUGH 153 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 154 THROUGH 247 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 248 THROUGH 314 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 315 THROUGH 464 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 2 THROUGH 9 )
12	X-RAY DIFFRACTION	12	CHAIN 'D' AND (RESID 2 THROUGH 9 )

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