PDB-6euy: Structure of the midlink and cap-binding domains of influenza A p...

ID or keywords:

Entry

Database: PDB / ID: 6euy

Title

Structure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor

Components

Polymerase basic protein 2

Keywords

RNA BINDING PROTEIN / Influenza A polymerase PB2 subunit cap-binding domain cap-binding inhibitor

Function / homology

Function and homology information

cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription ...
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Cusack, S. / Gaudon, S.

Funding support

France, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2018
Title: Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.
Authors: Pflug, A. / Gaudon, S. / Resa-Infante, P. / Lethier, M. / Reich, S. / Schulze, W.M. / Cusack, S.

History

Deposition	Oct 31, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2018	Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6euy.cif.gz	345.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6euy.ent.gz	288.6 KB	Display	PDB format
PDBx/mmJSON format	6euy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6euy_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	6euy_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6euy_validation.xml.gz	29.7 KB	Display
Data in CIF	6euy_validation.cif.gz	38.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eu/6euy ftp://data.pdbj.org/pub/pdb/validation_reports/eu/6euy	HTTPS FTP

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Related structure data

Related structure data	6euvC 6euwC 6euxC 6evjC 6evkC 5fmmS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2hwo-2 3g5d-2 2jkq-d 6hvf-1 3uqf-1 6tg0-1 4mcv-2 4lgh-2 3f6x-2 2bbs-1 Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Polymerase basic protein 2

B: Polymerase basic protein 2

C: Polymerase basic protein 2

hetero molecules

99.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Polymerase basic protein 2

hetero molecules

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

2

B: Polymerase basic protein 2

hetero molecules

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

3

C: Polymerase basic protein 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.461, 112.322, 201.088
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	17
Space group name H-M	P222₁

#1: Protein	Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3 Mass: 32524.322 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Victoria/3/1975(H3N2)) Gene: PB2 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: P31345
#2: Chemical	ChemComp-BYB / (2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid Mass: 400.382 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₉H₁₈F₂N₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Crystals were obtained with A/H3N2 double domain at 15 mg/ml in 20 mM Tris pH 8, 150 mM NaCl, 5% glycerol, 2 mM beta-mercaptoethanolmixed with 5 mM of VX-787 mixed with 0.2 M ammonium sulphate, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 4, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 42728 / % possible obs: 98.2 % / Redundancy: 4.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.065 / Net I/σ(I): 9.36
Reflection shell	Highest resolution: 3 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.634 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 6839 / CC_1/2: 0.794 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FMM

5fmm

Resolution: 3→49.031 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 32.81

	R_factor	Num. reflection	% reflection
R_free	0.2632	2072	4.86 %
R_work	0.2333	-	-
obs	0.2347	42607	98.27 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→49.031 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6442	0	117	0	6559

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6675
X-RAY DIFFRACTION	f_angle_d	0.51	8999
X-RAY DIFFRACTION	f_dihedral_angle_d	12.127	4086
X-RAY DIFFRACTION	f_chiral_restr	0.042	1041
X-RAY DIFFRACTION	f_plane_restr	0.003	1160

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 (%)
3-3.0698	0.5515	118	0.4096	2767	X-RAY DIFFRACTION	99
3.0698-3.1465	0.3791	138	0.3717	2711	X-RAY DIFFRACTION	99
3.1465-3.2316	0.3476	159	0.3479	2704	X-RAY DIFFRACTION	99
3.2316-3.3267	0.3927	137	0.3389	2742	X-RAY DIFFRACTION	99
3.3267-3.434	0.3245	131	0.3107	2669	X-RAY DIFFRACTION	98
3.434-3.5567	0.3212	131	0.2887	2677	X-RAY DIFFRACTION	96
3.5567-3.6991	0.3207	155	0.2485	2661	X-RAY DIFFRACTION	99
3.6991-3.8674	0.2766	157	0.2514	2755	X-RAY DIFFRACTION	99
3.8674-4.0712	0.3112	148	0.2519	2706	X-RAY DIFFRACTION	99
4.0712-4.3261	0.3221	134	0.2228	2697	X-RAY DIFFRACTION	99
4.3261-4.6599	0.2169	141	0.1852	2682	X-RAY DIFFRACTION	98
4.6599-5.1284	0.2075	154	0.1915	2673	X-RAY DIFFRACTION	97
5.1284-5.8694	0.2909	133	0.2104	2689	X-RAY DIFFRACTION	98
5.8694-7.3908	0.2227	132	0.2227	2726	X-RAY DIFFRACTION	99
7.3908-49.0372	0.1711	104	0.1914	2676	X-RAY DIFFRACTION	96

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	2.9431	-0.787	1.7148	5.8324	-1.6057	3.0239	-0.2054	-0.1799	0.0125	-0.2549	0.1523	-0.0141	-0.5836	-0.0765	-0.0289	0.664	0.0238	0.0149	0.7561	-0.1311	0.7042	14.7277	34.2807	417.2338
2	2.1453	-0.5074	0.25	3.7686	-3.1633	3.9052	-0.4945	0.2641	-0.627	-0.8716	-0.0398	-0.4633	0.7798	-0.3766	-0.0188	1.2954	-0.0943	0.2175	0.7863	-0.2695	0.8013	20.3653	17.1108	396.5904
3	1.0583	0.2797	-2.197	1.7809	-1.2819	4.4726	-0.4149	0.3115	-0.0782	-1.1625	-0.3992	-0.9133	1.196	0.2305	0.0695	1.4212	-0.0309	0.3561	0.8515	-0.1989	1.1355	27.9615	20.6867	392.607
4	3.1357	-0.0417	0.6603	6.3692	2.0794	2.7249	-0.498	0.4192	-0.3797	-1.4178	0.3526	-0.4128	0.0975	-0.1626	-0.0132	0.6657	0.0101	-0.0242	0.7396	-0.13	0.6908	16.336	29.0082	414.1426
5	1.7115	-0.2825	2.3102	4.7567	0.3352	2.7479	0.0653	-0.0669	-0.9865	1.2238	0.6144	-1.0409	1.5407	0.5035	0.1302	0.9869	0.2339	-0.2203	0.8448	-0.2899	1.522	35.7893	40.8366	431.5652
6	2.8017	1.5363	0.1913	5.1154	-1.1098	2.2533	-0.5154	0.4485	-0.7663	2.1255	1.0794	0.4225	-1.3202	-0.5591	-0.2039	1.4341	0.4545	-0.0942	1.3021	-0.0946	0.9254	21.2308	62.6958	435.799
7	4.6911	-3.1104	-0.3323	4.6203	-1.0906	2.0558	-0.5216	0.0251	0.2278	1.406	0.5847	-0.7105	-1.2683	-0.0487	0.1338	1.3994	0.1533	-0.3089	0.9244	-0.1932	0.815	29.7527	67.5001	437.9714
8	2.0306	-1.8574	-0.9806	6.7521	1.1015	2.7507	0.1816	0.136	-0.523	-2.1435	-0.6103	-3.333	-0.2444	0.7832	0.121	1.3994	0.0539	0.2958	1.7023	-0.1466	1.1612	34.3413	63.8704	420.1361
9	1.9172	0.3052	1.1508	4.3545	0.113	0.6462	-0.1441	-0.3854	1.0635	0.5993	0.3596	-1.0934	-0.7866	0.5757	0.011	1.4113	-0.025	-0.1307	1.0907	-0.3042	1.3098	35.0647	72.7612	433.1825
10	2.1148	-0.6515	-1.0324	0.203	0.0691	2.641	-0.1909	-1.0409	-0.1216	0.6159	0.5906	-1.17	-0.8063	0.7245	0.1112	1.7811	0.0847	-0.448	1.4381	-0.2293	1.1259	34.5868	69.2259	447.5704
11	3.412	1.1976	0.4746	4.277	-0.0198	3.1618	0.4344	0.0409	-0.3009	-0.5464	0.4078	-1.0246	-0.035	0.2331	0.1377	0.8336	0.0449	0.0679	0.8029	-0.324	1.2437	33.1492	47.0011	429.5458
12	2.8894	-0.6208	1.6312	2.5761	-0.9425	6.1939	0.1736	-0.6386	0.6201	1.2512	-0.106	-0.053	-0.4765	-0.4067	-0.0585	0.7816	-0.1611	0.1297	1.0646	-0.2994	0.9194	7.7593	21.7745	437.4989
13	0.526	-0.0649	-0.2382	4.4521	-0.686	1.9592	0.1582	0.0765	-0.0868	-0.9302	0.0363	-0.3558	0.1138	-0.0765	-0.1027	1.0482	-0.0938	-0.0097	0.9803	-0.1452	0.7983	9.3329	6.3998	423.9178
14	4.5218	0.3039	3.4021	4.0961	-1.4685	4.6229	0.5553	-0.4324	-0.6399	-0.7545	0.2574	0.2744	0.1802	-0.3146	-0.198	0.8513	-0.1882	-0.0229	0.9145	-0.0298	0.7446	2.0771	-5.0202	424.7666
15	4.8379	-0.8762	2.8566	4.0105	-1.9663	2.5141	0.1971	-0.801	-0.8691	-0.3735	0.3816	0.6239	0.6506	-0.9088	-0.2903	1.3861	-0.2606	-0.1676	1.2064	0.0816	0.9753	-4.6474	-7.3932	425.9371
16	2.6408	0.246	0.4241	6.1671	0.8301	4.6207	0.1751	-0.0565	0.03	-1.0019	-0.2994	-0.0457	-0.1171	-0.0667	-0.1092	0.7054	-0.0304	-0.0272	0.8313	-0.18	0.732	10.2797	12.3559	424.1478
17	1.0682	1.29	1.4652	2.7708	1.9625	2.2753	0.6336	-1.2023	-0.8621	0.2999	0.6008	0.0825	0.4119	-0.3003	-0.0257	1.3555	0.1027	0.1916	1.4985	-0.3888	1.4267	2.0679	19.3121	444.4386

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 252 through 327 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 328 through 413 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 414 through 490 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 491 through 533 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 252 through 327 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 328 through 345 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 346 through 413 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 414 through 429 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 430 through 453 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 454 through 496 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 497 through 532 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 252 through 305 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 306 through 345 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 346 through 405 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 406 through 488 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 489 through 517 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 518 through 532 )

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