PDB-5cfo: Crystal structure of anemone STING (Nematostella vectensis) in ap...

ID or keywords:

Entry

Database: PDB / ID: 5cfo

Title

Crystal structure of anemone STING (Nematostella vectensis) in apo 'rotated' open conformation

Components

Stimulator of Interferon Genes

Keywords

IMMUNE SYSTEM / STING / cyclic-dinucleotide binding domain

Function / homology

Function and homology information

2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of macroautophagy / autophagosome assembly / autophagosome / positive regulation of type I interferon production / activation of innate immune response / defense response to virus / innate immune response / endoplasmic reticulum membrane
Similarity search - Function

Biological species

Nematostella vectensis (starlet sea anemone)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.102 Å

Authors

Kranzusch, P.J. / Wilson, S.C. / Lee, A.S.Y. / Berger, J.M. / Doudna, J.A. / Vance, R.E.

Funding support

United States, 2items

Organization	Grant number	Country
Howard Hughes Medical Institute (HHMI)		United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI063302	United States

Citation

Journal: Mol.Cell / Year: 2015
Title: Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling.
Authors: Kranzusch, P.J. / Wilson, S.C. / Lee, A.S. / Berger, J.M. / Doudna, J.A. / Vance, R.E.

History

Deposition	Jul 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 9, 2015	Group: Database references
Revision 1.2	Sep 30, 2015	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5cfo.cif.gz	169.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5cfo.ent.gz	134.6 KB	Display	PDB format
PDBx/mmJSON format	5cfo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5cfo_validation.pdf.gz	421.9 KB	Display	wwPDB validaton report
Full document	5cfo_full_validation.pdf.gz	423.6 KB	Display
Data in XML	5cfo_validation.xml.gz	16.7 KB	Display
Data in CIF	5cfo_validation.cif.gz	23.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/5cfo ftp://data.pdbj.org/pub/pdb/validation_reports/cf/5cfo	HTTPS FTP

-
Related structure data

Related structure data	5cflC 5cfmC 5cfnC 5cfpC 5cfqC 5cfrC C: citing same article (ref.)
Similar structure data	6cca-d 6p3q-1 5cfn-d 4npr-3 6p3q-2 4egv-3 7m1a-d 4kbx-d 6yjk-d 4etz-2 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: Stimulator of Interferon Genes

B: Stimulator of Interferon Genes

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	82.296, 82.296, 100.346
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Stimulator of Interferon Genes / Predicted protein Mass: 23485.658 Da / Num. of mol.: 2 / Fragment: UNP Residues 178-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nematostella vectensis (starlet sea anemone) Gene: v1g246111 / Production host: Escherichia coli (E. coli) / References: UniProt: A7SLZ2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 4.18 Å³/Da / Density % sol: 70.55 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium citrate pH 7.0

-
Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11587 Å / Relative weight: 1
Reflection	Resolution: 2.1→41.15 Å / Num. obs: 43684 / % possible obs: 98.4 % / Redundancy: 11.3 % / R_merge(I) obs: 0.044 / Net I/σ(I): 9.4
Reflection shell	Resolution: 2.1→2.16 Å / Redundancy: 8.1 % / R_merge(I) obs: 0.882 / Mean I/σ(I) obs: 1 / % possible all: 81.1

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.102→41.148 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2018	1984	4.57 %	Random selection
R_work	0.1722	-	-	-
obs	0.1735	43378	97.95 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.102→41.148 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3006	0	0	209	3215

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3078
X-RAY DIFFRACTION	f_angle_d	1.322	4148
X-RAY DIFFRACTION	f_dihedral_angle_d	14.984	1178
X-RAY DIFFRACTION	f_chiral_restr	0.072	434
X-RAY DIFFRACTION	f_plane_restr	0.008	534

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 (%)
2.102-2.1541	0.3141	102	0.3006	2175	X-RAY DIFFRACTION	72
2.1541-2.2123	0.2818	138	0.2579	3029	X-RAY DIFFRACTION	100
2.2123-2.2774	0.2615	150	0.2332	3037	X-RAY DIFFRACTION	100
2.2774-2.3509	0.2303	146	0.2243	3021	X-RAY DIFFRACTION	100
2.3509-2.4349	0.2285	138	0.2049	2981	X-RAY DIFFRACTION	100
2.4349-2.5324	0.2441	147	0.211	3020	X-RAY DIFFRACTION	100
2.5324-2.6476	0.26	144	0.2147	3056	X-RAY DIFFRACTION	100
2.6476-2.7872	0.2437	135	0.216	2980	X-RAY DIFFRACTION	100
2.7872-2.9617	0.2561	150	0.2142	3051	X-RAY DIFFRACTION	100
2.9617-3.1903	0.2626	140	0.2035	2996	X-RAY DIFFRACTION	100
3.1903-3.5112	0.1882	156	0.1752	3006	X-RAY DIFFRACTION	100
3.5112-4.019	0.1677	142	0.1481	3011	X-RAY DIFFRACTION	100
4.019-5.062	0.1448	150	0.1209	3005	X-RAY DIFFRACTION	100
5.062-41.1559	0.1851	146	0.1421	3026	X-RAY DIFFRACTION	100

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	0.2584	-0.2079	0.0782	1.1669	0.395	0.1927	0.245	-0.0408	0.0067	0.2034	-0.2802	0.4451	0.4855	-0.2863	0.0009	0.4416	-0.0573	0.0163	0.3811	-0.0103	0.4163	-15.4025	-23.1905	-21.1977
2	0.5605	0.2173	-0.1141	0.428	-0.1918	0.0634	0.2685	-0.4957	-0.5872	0.1177	0.0747	-0.452	0.4267	-0.102	0.0008	0.5722	-0.0449	-0.0859	0.3713	-0.0078	0.4591	0.9746	-22.6056	-9.6696
3	0.4328	0.1831	0.1129	0.3974	-0.0764	0.0792	0.1401	0.1146	-0.0576	0.3294	-0.0939	-0.309	0.2154	-0.076	0.0001	0.5118	-0.0701	-0.0941	0.3449	-0.0118	0.5473	7.5577	-11.5577	-3.5425
4	0.537	0.0622	-0.0005	0.0756	0.2754	0.6069	0.2451	0.2925	0.3082	0.0857	-0.1578	0.2413	-0.3093	0.2359	-0.0002	0.5432	0.0115	-0.0261	0.4343	0.0613	0.4219	-5.4075	-7.8931	-21.5353
5	3.0915	0.9919	-0.3084	0.4317	0.2258	1.0406	-0.1285	0.3711	0.1058	-0.6715	0.3505	-0.6116	-0.1549	0.0626	0.0078	0.6012	-0.1087	-0.0492	0.4465	0.0049	0.5484	3.8894	-8.8146	-16.5628
6	0.0888	-0.2084	0.0476	0.4491	0.2065	0.2473	0.1429	0.2061	-0.5153	-0.1978	-0.0093	-0.0205	0.3572	0.174	-0.0002	0.7164	-0.038	-0.0347	0.3937	-0.156	0.7316	3.1149	-28.0811	-20.8124
7	0.2888	0.0719	0.3781	0.0755	0.076	0.3506	-0.3017	0.1624	0.3113	-0.2564	-0.0142	-0.0792	-0.5112	-0.0262	-0.0018	0.5148	-0.0547	-0.0837	0.2701	-0.0174	0.4902	2.8939	-4.4588	-9.7896
8	1.8904	0.8197	0.5946	2.1493	-1.4119	1.5233	0.1458	-0.0275	0.1949	0.0912	-0.0275	0.4199	-0.1232	-0.4158	-0	0.4303	0.0569	0.055	0.3647	0.0064	0.4021	-16.896	-14.1755	-25.2242
9	1.826	0.5061	0.6524	0.4966	0.5846	0.6577	-0.0314	-0.4677	0.3077	0.463	0.1273	0.1605	-0.2446	-0.6003	0.0008	0.5826	-0.0304	0.0426	0.46	-0.0315	0.406	-9.944	-11.4946	-11.2125
10	0.5021	0.3492	0.3251	0.4831	0.3966	0.3156	-0.2017	-0.5939	0.554	0.4842	0.0212	-0.4138	-0.3154	-0.6487	0.0007	0.6198	0.0085	-0.0148	0.5036	-0.1045	0.5106	-5.4531	-3.4016	-5.7622
11	0.2425	0.294	0.0266	1.1855	0.6158	0.3323	0.211	0.117	0.3137	-0.3514	-0.2454	0.4275	-0.5182	-0.3575	0.0001	0.4403	0.0644	-0.0236	0.3773	-0.0244	0.3969	-15.3005	-24.3018	-30.7842
12	1.2094	0.0315	-0.82	0.866	-0.2958	0.4334	0.2413	0.1248	0.0504	-0.3012	-0.1067	-0.3865	-0.342	-0.041	0.0001	0.4889	0.0593	0.065	0.2932	-0.0137	0.4273	3.955	-29.9156	-45.1367
13	0.3643	0.09	0.3584	0.0223	0.1757	0.5122	0.2081	-0.3354	-0.1983	-0.1974	-0.1185	0.2769	0.3102	0.2131	-0.0001	0.4972	-0.0042	0.0395	0.4365	0.0676	0.3665	-5.4034	-39.6287	-30.485
14	2.38	-0.9659	0.0741	0.5141	0.0037	1.0156	-0.1174	-0.3947	-0.0685	0.6871	0.4065	-0.4286	0.1016	0.0595	0.0095	0.5463	0.0982	0.025	0.4383	0.0334	0.5143	3.8879	-38.7125	-35.4279
15	0.1897	0.2774	0.0548	0.2685	0.1637	0.2181	0.155	-0.2311	0.6631	0.3378	-0.2528	-0.1017	-0.1328	0.1677	-0.0083	0.6309	0.0176	0.0393	0.3892	-0.1439	0.7098	3.1139	-19.4661	-31.1486
16	0.3673	0.0321	-0.4993	0.1051	0.0166	0.4598	-0.289	-0.1368	-0.2155	0.2918	0.0245	-0.0847	0.5435	-0.081	-0.0001	0.5385	0.0487	0.0962	0.2952	-0.0189	0.4925	2.8967	-43.0582	-42.2113
17	1.719	-0.9388	-0.2545	2.021	-1.348	1.4005	0.2198	0.0215	-0.1721	-0.0978	-0.0488	0.4636	0.2263	-0.2597	0.0001	0.4089	-0.0577	-0.05	0.3647	0.0076	0.3914	-16.9016	-33.3373	-26.7833
18	1.9224	-0.437	-0.3812	0.5894	0.6654	0.7527	-0.054	0.6148	-0.3812	-0.6267	0.1867	0.005	0.3061	-0.736	0.0044	0.5812	0.0098	-0.0536	0.4587	-0.0394	0.4069	-9.8723	-36.0949	-40.8745
19	0.641	-0.4646	-0.5121	0.3385	0.3525	0.3898	-0.1928	0.726	-0.7336	-0.6229	0.1115	-0.2154	0.3953	-0.7224	-0.0002	0.6214	-0.0135	0.026	0.5342	-0.1297	0.5432	-5.445	-44.0975	-46.2517

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 192 through 204 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 205 through 220 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 221 through 233 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 234 through 249 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 250 through 271 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 272 through 282 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 283 through 302 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 303 through 341 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 342 through 359 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 360 through 373 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 192 through 204 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 205 through 233 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 234 through 249 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 250 through 271 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 272 through 282 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 283 through 302 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 303 through 341 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 342 through 359 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 360 through 373 )

-
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