PDB-6xb6: Structure of Danaus plexippus poxin cGAMP nuclease

ID or keywords:

Entry

Database: PDB / ID: 6xb6

Title

Structure of Danaus plexippus poxin cGAMP nuclease

Components

Poxin

Keywords

HYDROLASE / Poxin / nuclease / Monarch / Butterfly / Moth / Lepidoptera / HDD13 / innate immunity / cGAS / cGAMP / STING

Function / homology

Poxin, virus / nuclease activity / 2',3'-cyclic GMP-AMP binding / Immune-related Hdd13

Function and homology information

Biological species

Danaus plexippus (monarch butterfly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.45 Å

Authors

Eaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.

Citation

Journal: Elife / Year: 2020
Title: Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host-pathogen conflict.
Authors: Eaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.

History

Deposition	Jun 5, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6xb6.cif.gz	356.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6xb6.ent.gz	242.5 KB	Display	PDB format
PDBx/mmJSON format	6xb6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6xb6_validation.pdf.gz	424.9 KB	Display	wwPDB validaton report
Full document	6xb6_full_validation.pdf.gz	427.6 KB	Display
Data in XML	6xb6_validation.xml.gz	25.6 KB	Display
Data in CIF	6xb6_validation.cif.gz	39.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xb/6xb6 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xb6	HTTPS FTP

-
Related structure data

Related structure data	6xb3C 6xb4C 6xb5C C: citing same article (ref.)
Similar structure data	5lwb-d 5fyb-d 6ek6-d 6h50-d 6gm3-2 5uuu-d 1hwo-d 4zdn-d 5oef-1 5fy9-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Poxin

B: Poxin

54.9 kDa, 2 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)	44.162, 75.414, 77.422
Angle α, β, γ (deg.)	90.000, 100.061, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	SER	SER	(chain 'A' and (resid 3 through 99 or resid 101...	A	A	3 - 99	4 - 100
1	2	ASP	ASP	VAL	VAL	(chain 'A' and (resid 3 through 99 or resid 101...	A	A	101 - 104	102 - 105
1	3	TRP	TRP	VAL	VAL	(chain 'A' and (resid 3 through 99 or resid 101...	A	A	107 - 132	108 - 133
1	4	SER	SER	LEU	LEU	(chain 'A' and (resid 3 through 99 or resid 101...	A	A	134 - 241	135 - 242
2	1	LYS	LYS	SER	SER	(chain 'B' and (resid 3 through 99 or resid 101...	B	B	3 - 99	4 - 100
2	2	ASP	ASP	VAL	VAL	(chain 'B' and (resid 3 through 99 or resid 101...	B	B	101 - 104	102 - 105
2	3	TRP	TRP	VAL	VAL	(chain 'B' and (resid 3 through 99 or resid 101...	B	B	107 - 132	108 - 133
2	4	SER	SER	LEU	LEU	(chain 'B' and (resid 3 through 99 or resid 101...	B	B	134 - 241	135 - 242

#1: Protein	Poxin / Immune-related Hdd13 Mass: 27441.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danaus plexippus (monarch butterfly) / Gene: HDD13, KGM_207136 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A212FM92
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 200 mM ammonium citrate, 25% PEG-3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 1.45→38.12 Å / Num. obs: 87244 / % possible obs: 98.6 % / Redundancy: 3.4 % / B_iso Wilson estimate: 15.2 Å² / CC_1/2: 0.996 / R_pim(I) all: 0.051 / Net I/σ(I): 7.2
Reflection shell	Resolution: 1.45→1.47 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4135 / CC_1/2: 0.441 / R_pim(I) all: 0.715

-
Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.45→38.12 Å / SU ML: 0.1548 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6585

	R_factor	Num. reflection	% reflection
R_free	0.1743	4203	4.88 %
R_work	0.1569	81997	-
obs	0.1578	86200	97.36 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→38.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3818	0	0	640	4458

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0126	3929
X-RAY DIFFRACTION	f_angle_d	1.1742	5335
X-RAY DIFFRACTION	f_chiral_restr	0.0951	584
X-RAY DIFFRACTION	f_plane_restr	0.0093	695
X-RAY DIFFRACTION	f_dihedral_angle_d	18.3872	1479

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 (%)
1.45-1.47	0.3251	106	0.2957	2063	X-RAY DIFFRACTION	73.88
1.47-1.48	0.2828	133	0.2361	2605	X-RAY DIFFRACTION	93.99
1.48-1.5	0.2327	137	0.2257	2677	X-RAY DIFFRACTION	95.98
1.5-1.52	0.2295	139	0.2208	2717	X-RAY DIFFRACTION	95.65
1.52-1.54	0.2343	137	0.2134	2684	X-RAY DIFFRACTION	97.21
1.54-1.56	0.2297	141	0.2038	2742	X-RAY DIFFRACTION	98.46
1.56-1.58	0.2201	143	0.2008	2789	X-RAY DIFFRACTION	98.72
1.58-1.61	0.2258	140	0.1941	2740	X-RAY DIFFRACTION	98.97
1.61-1.63	0.2359	141	0.1891	2784	X-RAY DIFFRACTION	98.75
1.63-1.66	0.2035	141	0.1948	2725	X-RAY DIFFRACTION	98.39
1.66-1.69	0.2663	136	0.1939	2758	X-RAY DIFFRACTION	97.24
1.69-1.72	0.2056	147	0.1839	2713	X-RAY DIFFRACTION	96.33
1.72-1.75	0.2153	144	0.1789	2767	X-RAY DIFFRACTION	99.52
1.75-1.79	0.2083	141	0.1706	2771	X-RAY DIFFRACTION	99.49
1.79-1.83	0.1996	144	0.1687	2790	X-RAY DIFFRACTION	99.42
1.83-1.87	0.1784	146	0.1634	2790	X-RAY DIFFRACTION	99.59
1.87-1.92	0.178	128	0.1602	2800	X-RAY DIFFRACTION	99.12
1.92-1.97	0.1872	153	0.1585	2745	X-RAY DIFFRACTION	98.98
1.97-2.03	0.1727	132	0.1534	2786	X-RAY DIFFRACTION	98.45
2.03-2.09	0.1704	140	0.1472	2728	X-RAY DIFFRACTION	97.75
2.09-2.17	0.1621	157	0.1433	2643	X-RAY DIFFRACTION	95.56
2.17-2.25	0.1951	143	0.1484	2808	X-RAY DIFFRACTION	99.73
2.25-2.35	0.168	126	0.1397	2840	X-RAY DIFFRACTION	99.76
2.35-2.48	0.1758	153	0.1475	2793	X-RAY DIFFRACTION	99.46
2.48-2.63	0.1735	130	0.1584	2795	X-RAY DIFFRACTION	99.12
2.63-2.84	0.1827	151	0.1527	2767	X-RAY DIFFRACTION	98.51
2.84-3.12	0.1484	141	0.1513	2702	X-RAY DIFFRACTION	95.5
3.12-3.57	0.1585	134	0.1422	2826	X-RAY DIFFRACTION	99.93
3.57-4.5	0.1194	156	0.1245	2829	X-RAY DIFFRACTION	99.73
4.5-38.12	0.1522	143	0.1516	2820	X-RAY DIFFRACTION	97.56

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	0.765961940332	-0.0495511318415	0.476192169784	0.348067910631	-0.354744278249	0.50482823344	0.148340279958	0.0253236322272	-0.178620792793	-0.103666810915	0.0284311773565	0.117685298573	0.3238146557	-0.0194111214892	0.00949917155755	0.162168254724	-0.00773264031093	-0.0216755296055	0.126789790088	-0.000835693949465	0.150335699655	-5.56290849343	-37.3980397834	17.8002312819
2	0.431496568885	-0.109378869894	0.43690777509	0.133168730848	-0.0498396165002	0.466562509792	0.104430246683	0.0500859970922	0.00571276958373	0.0214466876571	-0.109823015543	-0.0281210449165	0.0956948889773	0.143508132484	-0.00559946169035	0.10087807405	0.00904384928883	-0.000557494380524	0.124617398828	0.00991737928075	0.121164460835	8.21093851499	-29.5883037452	29.4365271218
3	0.421299776524	0.0523630081757	0.468499414369	0.465137391816	0.0621589921205	1.08108365339	-0.0068133950971	0.128947300905	0.0198805418625	-0.0596145119256	0.0176156865628	-0.0158120391222	0.0193886104377	0.166930782418	-0.00103126947169	0.0847442177895	0.00103336814132	0.0103576594223	0.104990917127	-0.0035259351692	0.0939004667109	2.45796906424	-24.9554793571	14.8754917771
4	0.588000334169	0.26144503402	0.553233844529	0.663938724676	0.100381805548	0.917586007545	0.00215920346183	0.10569981307	-0.019922158154	-0.0529454499406	0.0163430407536	-0.00445705162855	0.0192941191002	0.0846609589492	0.00567587623306	0.0850516966816	0.00425034822027	0.0187483101039	0.116119348008	0.00194954125661	0.103770954129	1.44262336449	-23.5356796698	19.9458009878
5	0.455546444093	-0.0481750504836	-0.297705977557	0.813466860891	0.259988917758	0.475539183334	0.00930187463034	-0.0275715733762	0.103932386996	0.0518265323427	-0.0337804395725	0.123889037433	-0.0141999629841	-0.0740875341011	-0.0001754502385	0.112304174294	0.00943799725217	-0.00222778820984	0.0999312967608	-0.0192733782229	0.161013425265	2.09412191113	1.34781758351	38.5957635233
6	0.258145084985	0.442675348228	0.00669557648972	0.732597886425	0.113697213046	0.319145690021	-0.0497408921054	-0.0236431377499	0.0640693360748	-0.0455394527293	0.0201782650736	0.104649784786	-0.0685990157469	-0.0621039387502	-0.00209258740354	0.0906300541463	0.00679483942423	-0.000425237754524	0.0982088259375	-0.000154011737955	0.136128803206	0.670111297782	-8.18186888037	28.5010058916
7	0.294193578248	-0.030234080114	-0.274841909373	0.512061393706	0.138305750846	0.291893050304	-0.104023447487	0.331336889667	0.325979131599	-0.178347836261	-0.0803343108456	0.0689956905184	-0.586648116926	0.0634199734822	-0.0960368859314	0.31944717793	-0.0695584579003	-0.00861112272702	0.193129081235	0.049215557804	0.15873146058	16.922060388	22.1004000499	1.24668922577
8	-0.0585016816303	-0.153217336013	0.0184729063134	0.390761097828	-0.114496614801	1.62316137819	-0.0157892308594	-0.0760543570368	0.0614622756678	-0.0181935203723	-0.090739346032	-0.0067014628043	-0.280315423752	-0.114369561908	-0.343388755227	0.167000801244	0.000887131096794	-0.0031911505637	0.142447181416	-0.00394682199818	0.116194732082	11.9934528262	17.892945466	17.4673120454
9	0.102088057611	-0.082336687854	0.00884780431893	0.256972236554	-0.236964727562	0.190434926439	0.00450425356294	0.0561951557481	-0.00895421219345	-0.0888728394398	-0.0056505059135	0.068970352175	-0.0261773084456	-0.0874735301698	0.000844664482352	0.133952315126	-0.0101753509704	-0.00665852863151	0.120645740554	0.00573795435191	0.122866888764	11.4255604867	3.40429329615	15.9719834942
10	0.12931093641	-0.0470786739783	0.0626902467094	0.283324381192	-0.0948064221552	1.0476843306	-0.00674467167345	0.0151636882907	-0.0181919682329	-0.0294964617404	-0.0253041013723	-0.0287762445688	-0.0892288456074	-0.119027659989	-0.0249647703345	0.114877815976	-0.00351301578634	0.00343529978831	0.131429619445	-0.000798277093015	0.108738840234	12.6605039879	8.82512741934	15.3402020611
11	0.183453301861	-0.0532267062969	-0.069864262723	0.258282130123	-0.148471321023	0.0992123462568	0.00584885086234	0.196882966563	0.112546632102	-0.275731924279	-0.0554981414216	-0.0332762418705	-0.0273108855842	-0.157176129112	2.68267982825E-5	0.141322955215	0.00206611265802	0.0106410129227	0.146628443774	-0.00992506198547	0.166469870976	26.2626618712	-16.2037530042	21.5873256972
12	0.387953897532	0.132605783794	-0.0716760239399	0.134575671637	0.143680785401	0.554989465094	-0.135989100815	-0.108361587221	-0.0391414824411	0.21698496224	0.0477907680478	-0.066829639405	0.0956236856656	0.11368519956	-0.110437826282	0.132307321426	0.0192746691914	0.0116471196907	0.118233571507	0.021587245227	0.153769293406	23.4491111133	-15.4627284197	35.2549212204
13	0.234822334801	-0.0132440899932	0.293719009186	0.742586738609	-0.153586597569	0.307731493268	0.000650751838245	0.0982880860866	-0.0197652639137	-0.0972089708321	0.0092149489942	-0.0627176812093	0.0724195203676	0.0923575210289	0.0110025081494	0.0971272283462	0.00223250556981	0.0230086167871	0.140994244943	0.00606179300389	0.116755313401	18.8649341456	-6.44600043123	21.1622658794

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 65 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 114 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 115 through 166 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 167 through 203 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 204 through 241 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 14 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 15 through 88 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 89 through 114 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 115 through 166 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 167 through 181 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 182 through 203 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 204 through 241 )

-
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