PDB-8t5w: Influenza PAN endonuclease I38T mutant with Baloxavir

ID or keywords:

Entry

Database: PDB / ID: 8t5w

Title

Influenza PAN endonuclease I38T mutant with Baloxavir

Components

Polymerase acidic protein

Keywords

VIRAL PROTEIN / HYDROLASE/INHIBITOR / Influenza endonuclease / resistance / drug discovery / metal-binding pharmacophore / ANTIVIRAL PROTEIN / HYDROLASE-INHIBITOR complex

Function / homology

Function and homology information

cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Kohlbrand, A.J. / Cohen, S.M.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2024
Title: Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants.
Authors: Kohlbrand, A.J. / Stokes, R.W. / Sankaran, B. / Cohen, S.M.

History

Deposition	Jun 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8t5w.cif.gz	112.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8t5w.ent.gz	72.2 KB	Display	PDB format
PDBx/mmJSON format	8t5w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8t5w_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8t5w_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8t5w_validation.xml.gz	11 KB	Display
Data in CIF	8t5w_validation.cif.gz	14.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t5/8t5w ftp://data.pdbj.org/pub/pdb/validation_reports/t5/8t5w	HTTPS FTP

-
Related structure data

Related structure data	8t5zC 8t67C 8t6zC 8t81C 8t94C 8vgzC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1)

Deposited unit

A: Polymerase acidic protein

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	75.111, 75.111, 121.444
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6₂22
Space group name Hall	P6₂2(x,y,z+1/3)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/3 #3: y,-x+y,z+2/3 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: x-y,-y,-z #7: -x,-x+y,-z+1/3 #8: -x,-y,z #9: y,x,-z+2/3 #10: -y,-x,-z+2/3 #11: -x+y,y,-z #12: x,x-y,-z+1/3

Components on special symmetry positions

ID	Model	Components
1	1	A-421- HOH

#1: Protein	Polymerase acidic protein / RNA-directed RNA polymerase subunit P2 Mass: 22412.494 Da / Num. of mol.: 1 / Mutation: I38T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1)) Strain: A/California/04/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-E4Z / Baloxavir acid Mass: 483.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₄H₁₉F₂N₃O₄S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.77 %
Crystal grow	Temperature: 306 K / Method: vapor diffusion, hanging drop Details: 32% PEG (MW 4000 g/mol), 100 mM Tris (pH 8.35), and 220 mM sodium acetate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→57.34 Å / Num. obs: 46072 / % possible obs: 99.9 % / Redundancy: 20.7 % / B_iso Wilson estimate: 32.56 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.054 / Net I/σ(I): 28
Reflection shell	Resolution: 1.65→1.71 Å / Num. unique obs: 2449 / CC_1/2: 0.861

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→57.34 Å / SU ML: 0.1999 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2339	3678	7.98 %
R_work	0.2019	42393	-
obs	0.2044	46071	99.84 %

Solvent computation

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

Displacement parameters

B_iso mean: 40.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→57.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1463	0	70	95	1628

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0086	1569
X-RAY DIFFRACTION	f_angle_d	1.5533	2118
X-RAY DIFFRACTION	f_chiral_restr	0.1061	217
X-RAY DIFFRACTION	f_plane_restr	0.0089	265
X-RAY DIFFRACTION	f_dihedral_angle_d	9.3885	204

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 (%)
1.65-1.67	0.3247	143	0.2958	1620	X-RAY DIFFRACTION	99.38
1.67-1.69	0.3303	141	0.2932	1615	X-RAY DIFFRACTION	99.55
1.69-1.72	0.3414	139	0.3065	1619	X-RAY DIFFRACTION	99.77
1.72-1.74	0.3776	147	0.3539	1651	X-RAY DIFFRACTION	99.78
1.74-1.77	0.3561	137	0.3323	1613	X-RAY DIFFRACTION	99.83
1.77-1.8	0.3306	142	0.2838	1632	X-RAY DIFFRACTION	99.89
1.8-1.83	0.3204	143	0.2776	1664	X-RAY DIFFRACTION	99.94
1.83-1.87	0.252	133	0.2711	1589	X-RAY DIFFRACTION	99.88
1.87-1.9	0.2966	143	0.2468	1632	X-RAY DIFFRACTION	100
1.9-1.94	0.2699	142	0.2322	1661	X-RAY DIFFRACTION	99.89
1.94-1.98	0.2181	148	0.2358	1623	X-RAY DIFFRACTION	99.89
1.98-2.03	0.247	142	0.2268	1640	X-RAY DIFFRACTION	100
2.03-2.08	0.248	138	0.2302	1630	X-RAY DIFFRACTION	100
2.08-2.14	0.2652	140	0.241	1633	X-RAY DIFFRACTION	99.94
2.14-2.2	0.3226	143	0.1946	1637	X-RAY DIFFRACTION	100
2.2-2.27	0.2302	145	0.2061	1620	X-RAY DIFFRACTION	100
2.27-2.35	0.2381	146	0.2204	1629	X-RAY DIFFRACTION	100
2.35-2.44	0.2381	136	0.2171	1624	X-RAY DIFFRACTION	100
2.44-2.56	0.2071	139	0.2118	1638	X-RAY DIFFRACTION	100
2.56-2.69	0.2562	139	0.2227	1641	X-RAY DIFFRACTION	99.89
2.69-2.86	0.254	144	0.221	1616	X-RAY DIFFRACTION	99.89
2.86-3.08	0.2608	141	0.2116	1632	X-RAY DIFFRACTION	100
3.08-3.39	0.2107	144	0.1905	1644	X-RAY DIFFRACTION	100
3.39-3.88	0.1932	143	0.1751	1642	X-RAY DIFFRACTION	100
3.88-4.89	0.1925	140	0.1468	1618	X-RAY DIFFRACTION	99.89
4.89-57.34	0.2347	140	0.1956	1630	X-RAY DIFFRACTION	98.55

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	4.38569531082	4.15807977857	-1.29934566384	4.58766396207	-2.45577486471	8.44485598641	-0.127575483053	1.40504036818	-1.39826932357	-0.680938312489	0.131156767731	-1.34826463856	1.07024361196	0.659875377467	-0.0709980519715	0.395653288554	0.0523769565915	-0.0206740429153	0.50674833634	-0.110350958889	0.451233583603	35.4808419559	6.19649838434	-17.2078947814
2	9.73512703952	-3.12608281589	3.95118041205	4.14937113047	-4.23528404941	4.56153184305	0.244916276693	1.07034246803	-0.441088174178	-0.970432653801	-0.157994093134	0.261498408087	0.758726230827	-0.384895815426	-0.0875607172427	0.383331081472	0.00632781496076	-0.00276965125465	0.398444623975	-0.0638468094914	0.359638706872	23.2060478208	5.51255626497	-19.588442028
3	7.67892592777	3.3002952195	-2.7502154373	7.5587217064	-2.59036586514	5.99935613548	0.191651142517	0.930195320047	0.527319768682	-0.908419578385	-0.217447849192	0.356429989549	-0.0538274401264	-1.77630818532	0.105096486403	0.425794093612	-0.000662604185495	-0.0488344315374	0.686742364581	-0.022710832062	0.216027328751	26.598464614	13.2910906804	-25.9725541357
4	9.02419670111	1.23819640969	-4.92131745517	2.25455892206	0.317943218547	3.10734612967	-0.00345158202975	0.237871485826	-0.16868705925	-0.0748829979388	0.00566721697707	0.00269846353601	0.131280672855	-0.230470139876	0.100248670773	0.245158353465	0.007426738772	-0.02476303986	0.25178616717	0.0126413471455	0.248396899762	25.4773364222	10.5987721341	-10.7164096631
5	6.51302463872	0.633509692927	0.201076092893	1.63629364944	0.163934893952	1.95624497504	0.0968756038574	-0.332906623268	0.0227002535353	0.0226845842491	-0.104195480872	0.345997776683	0.0348779686629	-0.386090259265	0.018395751677	0.229407963309	0.0367199391256	0.0200190840256	0.28597415524	0.0423653555037	0.271694892307	11.3640289392	13.9210784339	-7.83876745131
6	6.7830968667	-4.68150387971	3.33376264807	3.33406537022	-2.57044790529	7.0650505583	-0.205447556461	0.275612599912	1.16839805682	-0.384448723784	-0.296224440995	-0.305484999365	-0.553254595852	-0.129718888968	0.426561757733	0.3932146039	0.0120105342916	-0.0227923474947	0.249897389323	0.0187840146863	0.496677512308	20.9431111086	27.6639257526	-8.31291649686
7	7.27415056568	3.62961381417	-3.31114398068	4.66843657436	0.241106566927	7.32763399503	-0.554172894131	0.124674049721	0.957914384748	-0.0359863060507	0.418048457728	1.2089266344	-0.566606571426	-1.02238750012	0.17470662254	0.28702652769	0.0224847212503	0.0197331069357	0.349511283768	0.0135103767874	0.532557024229	16.2201053473	22.6875305976	-4.04967049521
8	2.932135103	-1.53913275123	-2.22043638093	4.73678929254	0.775220360377	6.74866471093	0.0143160932423	-1.02309248548	0.480195941855	0.214363501513	-0.00783270382608	-0.0225798916798	-0.319118646324	0.0917814167111	0.00892040773556	0.269269174377	0.00531021901245	-0.0137098685236	0.358164788062	-0.0408532996958	0.341846680838	23.3754276798	20.3730108456	2.17440595572
9	4.89315740817	-1.00337470792	-1.35108497754	4.92997969106	0.336310437811	4.7818722546	0.0173090645711	-0.291678961632	-0.205467560852	-0.000784681475974	-0.0462589273323	0.148923901972	0.175572065268	0.264197346393	0.0664012317992	0.214406384443	-0.00526801535081	-0.0517080268053	0.264597319006	0.0131083194879	0.242834858575	34.0922924723	12.0656889086	-2.84672208512
10	6.70324232968	-2.01382795519	1.85062050012	5.1929001381	-3.52351183072	7.57205332619	-0.103360685578	-0.13891982412	0.345772580926	0.274135629226	0.0632073845687	0.000860837212246	-0.945849162479	0.447698583341	0.0608977017284	0.323341083798	-0.00578092921464	0.0351215169984	0.299655668199	0.0753323027256	0.25816922674	36.5058878213	21.7089121655	-15.2875750928

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 10 )	-1 - 10	1 - 12
2	2	chain 'A' and (resid 11 through 23 )	11 - 23	13 - 25
3	3	chain 'A' and (resid 24 through 31 )	24 - 31	26 - 33
4	4	chain 'A' and (resid 32 through 50 )	32 - 50	34 - 52
5	5	chain 'A' and (resid 51 through 126 )	51 - 126	53 - 105
6	6	chain 'A' and (resid 127 through 138 )	127 - 138	106 - 117
7	7	chain 'A' and (resid 139 through 149 )	139 - 149	118 - 128
8	8	chain 'A' and (resid 150 through 164 )	150 - 164	129 - 143
9	9	chain 'A' and (resid 165 through 185 )	165 - 185	144 - 164
10	10	chain 'A' and (resid 186 through 197 )	186 - 197	165 - 176

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi