PDB-4nux: Structure of receptor A

ID or keywords:

Entry

Database: PDB / ID: 4nux

Title

Structure of receptor A

Components

Interleukin-17 receptor A

Keywords

IMMUNE SYSTEM / SEFIR domain / cytokine / receptor / autoimmune inflammatory

Function / homology

Function and homology information

interleukin-17 receptor activity / granulocyte chemotaxis / Interleukin-17 signaling / T-helper 17 type immune response / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.295 Å

Authors

Zhang, B. / Han, Y. / Deng, J.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved alpha-helix for Act1 binding and IL-17 signaling.
Authors: Zhang, B. / Liu, C. / Qian, W. / Han, Y. / Li, X. / Deng, J.

History

Deposition	Dec 4, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2014	Group: Database references
Revision 1.2	Feb 28, 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	4nux.cif.gz	95 KB	Display	PDBx/mmCIF format
PDB format	pdb4nux.ent.gz	73.8 KB	Display	PDB format
PDBx/mmJSON format	4nux.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4nux_validation.pdf.gz	408.8 KB	Display	wwPDB validaton report
Full document	4nux_full_validation.pdf.gz	410.6 KB	Display
Data in XML	4nux_validation.xml.gz	9.7 KB	Display
Data in CIF	4nux_validation.cif.gz	12.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nu/4nux ftp://data.pdbj.org/pub/pdb/validation_reports/nu/4nux	HTTPS FTP

-
Related structure data

Similar structure data	2a70-1 2biq-d 5qul-1 5g4n-2 4rhf-d 1ex7-d 6si2-1 2a70-2 5quk-d 4wb3-1 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: Interleukin-17 receptor A

24.8 kDa, 1 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)	76.256, 136.130, 55.433
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Interleukin-17 receptor A / IL-17 receptor A / IL-17RA / CDw217 Mass: 24771.557 Da / Num. of mol.: 1 / Fragment: SEFIR domain (UNP residues 376-591) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RA, IL17R / Production host: Escherichia coli (E. coli) / References: UniProt: Q96F46
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.64 %
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 6 Details: 0.1M MES, 5%PEG6000, pH 6.0, EVAPORATION, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2012

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. all: 13265 / Num. obs: 13104 / % possible obs: 98.7 % / Observed criterion σ(I): 2.3

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
2.3-2.34	4.8	1.6	559	1	87.3
6.24-50	6.6	52.9	740	1	99.7
4.95-6.24	6.8	35.8	687	1	100
4.33-4.95	6.9	37.6	673	1	100
3.93-4.33	7.1	31.1	669	1	100
3.65-3.93	7.1	26.6	676	1	100
3.44-3.65	7.2	21.9	661	1	100
3.26-3.44	7.2	20.4	657	1	100
3.12-3.26	7.2	14.7	665	1	100
3-3.12	7.2	10.8	658	1	100
2.9-3	7.3	8.8	652	1	100
2.81-2.9	7.3	7.6	655	1	100
2.73-2.81	7.3	5.4	661	1	100
2.66-2.73	7.2	5	663	1	100
2.59-2.66	7.3	3.8	634	1	100
2.53-2.59	7.1	3.6	654	1	100
2.48-2.53	6.6	3	663	1	100
2.43-2.48	5.9	2.4	649	1	99.8
2.38-2.43	5.3	2	626	1	97.4
2.34-2.38	4.3	1.6	602	1	91.5

-
Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHENIX	(phenix.refine: 1.6_289)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.295→33.264 Å / SU ML: 0.3 / σ(F): 0.26 / Phase error: 25.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2418	1220	10.06 %	10%
R_work	0.1893	-	-	-
obs	0.1948	12124	91.21 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.582 Å² / k_sol: 0.349 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.407 Å²	-0 Å²	-0 Å²
2-	-	-3.3092 Å²	0 Å²
3-	-	-	-6.0979 Å²

Refinement step

Cycle: LAST / Resolution: 2.295→33.264 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1579	0	0	54	1633

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1612
X-RAY DIFFRACTION	f_angle_d	1.066	2183
X-RAY DIFFRACTION	f_dihedral_angle_d	16.285	586
X-RAY DIFFRACTION	f_chiral_restr	0.073	233
X-RAY DIFFRACTION	f_plane_restr	0.004	283

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 (%)
2.2946-2.3864	0.3113	102	0.2404	928	X-RAY DIFFRACTION	71
2.3864-2.495	0.3048	130	0.2223	1083	X-RAY DIFFRACTION	84
2.495-2.6265	0.2833	134	0.2101	1168	X-RAY DIFFRACTION	89
2.6265-2.791	0.2943	126	0.2161	1189	X-RAY DIFFRACTION	90
2.791-3.0064	0.2895	141	0.2201	1236	X-RAY DIFFRACTION	94
3.0064-3.3086	0.2663	134	0.1924	1285	X-RAY DIFFRACTION	96
3.3086-3.7868	0.2226	146	0.1745	1293	X-RAY DIFFRACTION	98
3.7868-4.7688	0.1824	149	0.1476	1320	X-RAY DIFFRACTION	98
4.7688-33.268	0.2152	158	0.1781	1402	X-RAY DIFFRACTION	99

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	2.2169	-0.2651	0.6756	4.0827	-1.2924	0.5637	-0.5499	0.244	0.1826	-0.2648	0.4409	-0.1042	-0.1389	-0.4146	0.081	0.4058	0.1371	-0.1719	0.2352	0.0137	0.2659	38.2656	54.3339	27.6504
2	2.0154	0.5861	0.0416	1.1714	0.1385	0.0021	0.1936	-0.3139	0.0909	0.0253	-0.3115	-0.1535	0.2864	0.1623	0.0238	0.2025	0.0286	0.0153	0.238	0.0156	0.1097	49.8295	44.7101	39.1276
3	1.4406	0.5079	0.3513	1.5949	1.6809	2.0264	0.2001	-0.1984	0.2894	0.4806	-0.2503	0.3958	0.2135	-0.2771	-0.0091	0.139	0.0688	0.0078	0.1005	-0.0404	0.1087	41.9579	54.1829	36.539
4	2.4788	-1.1506	-2.2369	2.1001	-0.5945	4.2862	-0.3766	-0.8684	0.1199	0.3742	-0.0732	0.2263	0.0523	-1.3368	0.3929	0.3052	-0.0561	-0.0429	0.5798	0.033	0.408	34.8016	37.7007	34.7849
5	5.4377	0.0284	-1.4783	6.2409	-3.1559	2.073	-0.3574	1.0535	-0.8172	-0.0938	0.6699	0.2491	0.4438	-0.7925	-0.5711	0.1998	0.0387	-0.1376	0.4711	-0.0338	0.2982	37.3202	40.5098	25.1182
6	1.1752	0.9672	0.2352	2.1085	1.2024	1.1895	-0.5945	0.0503	0.1377	-0.5728	0.4421	0.1992	-0.7821	-0.3089	0.1977	0.4822	0.0839	-0.0342	0.2384	0.0565	0.2187	40.3637	50.7336	22.6003
7	3.6211	0.4964	-0.086	0.4766	-0.614	1.9046	0.0623	-0.3524	-0.4594	-0.0362	0.1202	-0.4857	0.328	0.0559	-0.0542	0.1586	0.0057	0.0661	0.1458	-0.0045	0.2064	57.2081	38.2146	28.6682
8	5.4235	-1.2888	1.7251	0.5908	0.2655	7.3039	0.2496	-0.5921	-1.4537	0.0821	-0.27	0.2325	0.6211	-0.1223	0.3338	0.1876	0.1247	0.0199	0.1502	-0.0671	0.2336	56.4978	30.1506	31.9596
9	3.3515	-1.4038	0.2882	6.8858	-2.7616	2.8889	0.479	0.4205	-0.1843	0.3344	-0.0141	0.1427	0.1576	0.0252	-0.3475	0.2444	0.0151	-0.0483	0.2082	0.0522	0.2198	48.3645	34.8782	37.6886
10	1.5226	-0.0328	-1.2415	1.4081	1.4291	2.3197	0.2767	0.46	-0.3148	0.0054	-0.1493	-0.2961	-0.5377	-0.3142	-0.0344	0.2514	0.0822	-0.0341	0.2579	-0.0347	0.1238	48.2834	40.9343	19.1642
11	1.4453	1.6969	1.3946	1.8928	1.3451	2.3718	-0.2194	0.212	0.1728	-0.3934	0.1255	-0.1765	-0.4357	0.3074	0.1189	0.1842	0.0468	-0.013	0.125	-0.024	0.1854	52.9383	51.0465	26.4911
12	1.5096	-0.4224	-1.2383	3.7017	0.0341	1.4083	0.2304	0.0635	-0.0412	-0.3375	-0.6506	0.1187	-0.0262	0.5425	0.3379	0.1788	0.0909	-0.0053	0.2068	-0.049	0.2666	59.2946	45.1478	26.2744
13	1.6142	-0.8796	1.6175	1.3769	0.2414	5.9372	-0.4698	0.3575	0.2568	-0.0124	-0.4768	-0.3123	-0.1733	0.7644	0.5268	0.3362	0.022	0.1209	0.2993	0.1415	0.21	56.5141	55.9925	27.718
14	4.0389	1.8691	2.718	5.2992	3.8848	8.3099	0.0604	-0.0757	0.7664	-0.9305	-1.0394	-0.3633	-2.1923	-0.1212	0.733	0.8505	0.0489	0.0247	0.1528	0.0633	0.2953	50.2476	62.8143	27.3409
15	3.6659	0.1979	-3.2961	0.6443	-0.6056	9.8303	-0.5098	0.3917	-0.2321	-0.7089	-0.1033	-0.5082	0.463	-0.5267	0.5863	0.3675	0.0468	0.1066	0.2071	0.0686	0.2565	44.8814	61.1834	23.4223
16	2.8603	0.2291	-0.2054	4.4087	1.5766	2.1874	0.4271	-0.6036	0.6123	0.6854	-0.2363	-1.114	0.5589	0.3946	-0.4851	0.3704	-0.036	0.1148	-0.0247	-0.0648	0.3359	52.526	65.6303	36.9091
17	1.8244	-0.2391	1.3542	1.8564	-1.2856	1.8252	-0.1884	-0.4791	0.5524	0.8965	0.0181	-0.4164	-0.6268	-0.0391	0.3362	0.2768	-0.0621	-0.0652	0.2087	-0.0426	0.107	53.7165	55.1098	45.1963
18	9.2244	6.672	-6.073	5.116	-4.3102	4.015	0.7888	-0.4729	0.2064	1.2402	-0.265	0.4634	0.1863	0.0052	-0.3308	0.2742	-0.0961	-0.1464	0.3083	0.0674	0.2528	62.8093	42.9893	47.9093
19	7.5492	-4.4085	-3.0786	4.8976	4.3806	4.1421	0.5745	-0.5337	-0.1536	-0.8185	1.0662	-0.8728	-0.1217	0.7197	-1.3322	0.3401	0.0623	0.0785	0.29	-0.037	0.3169	61.1949	37.0771	41.6224
20	3.2021	-2.2727	-1.1178	7.7099	5.7027	4.3592	0.4734	0.3923	0.6435	0.9636	-0.5551	-0.9653	1.6836	-0.3599	0.3398	0.3985	-0.0274	-0.0456	0.2017	0.0816	0.1948	56.2648	29.6189	40.8538

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 376:381)
2	X-RAY DIFFRACTION	2	(chain A and resid 382:396)
3	X-RAY DIFFRACTION	3	(chain A and resid 397:414)
4	X-RAY DIFFRACTION	4	(chain A and resid 415:425)
5	X-RAY DIFFRACTION	5	(chain A and resid 426:434)
6	X-RAY DIFFRACTION	6	(chain A and resid 435:445)
7	X-RAY DIFFRACTION	7	(chain A and resid 446:460)
8	X-RAY DIFFRACTION	8	(chain A and resid 461:467)
9	X-RAY DIFFRACTION	9	(chain A and resid 468:478)
10	X-RAY DIFFRACTION	10	(chain A and resid 479:493)
11	X-RAY DIFFRACTION	11	(chain A and resid 494:507)
12	X-RAY DIFFRACTION	12	(chain A and resid 508:517)
13	X-RAY DIFFRACTION	13	(chain A and resid 518:529)
14	X-RAY DIFFRACTION	14	(chain A and resid 530:534)
15	X-RAY DIFFRACTION	15	(chain A and resid 535:539)
16	X-RAY DIFFRACTION	16	(chain A and resid 540:560)
17	X-RAY DIFFRACTION	17	(chain A and resid 561:576)
18	X-RAY DIFFRACTION	18	(chain A and resid 577:582)
19	X-RAY DIFFRACTION	19	(chain A and resid 583:586)
20	X-RAY DIFFRACTION	20	(chain A and resid 587:591)

-
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