PDB-5jjn: Structure of the SRII/HtrII(G83F) Complex in P212121 space group ...

ID or keywords:

Entry

Database: PDB / ID: 5jjn

Title

Structure of the SRII/HtrII(G83F) Complex in P212121 space group ("V" shape)

Components

Sensory rhodopsin II transducer
Sensory rhodopsin-2

Keywords

SIGNALING PROTEIN / sensory rhodopsin II / transducer / membrane protein complex

Function / homology

Function and homology information

photoreceptor activity / phototransduction / monoatomic ion channel activity / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Natronomonas pharaonis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Ishchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J. / Remeeva, A. / Polovinkin, V. / Utrobin, P. / Balandin, T. ...

Funding support

Russian Federation, 1items

Citation

Journal: Sci Rep / Year: 2017
Title: New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex.
Authors: Ishchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J.P. / Remeeva, A. / Polovinkin, V. / Utrobin, P. / Balandin, T. / Engelhard, M. / Buldt, G. / Gordeliy, V.

History

Deposition	Apr 24, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5jjn.cif.gz	232.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5jjn.ent.gz	184.8 KB	Display	PDB format
PDBx/mmJSON format	5jjn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5jjn_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	5jjn_full_validation.pdf.gz	2.5 MB	Display
Data in XML	5jjn_validation.xml.gz	24.6 KB	Display
Data in CIF	5jjn_validation.cif.gz	32.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jj/5jjn ftp://data.pdbj.org/pub/pdb/validation_reports/jj/5jjn	HTTPS FTP

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Related structure data

Related structure data	5jjeC 5jjfC 5jjjC 1hs2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1h2s-1 1wcq-1 1euu-d 2ber-d 2bzd-3 1eut-d 3uyi-1 2bzd-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#27 - Mar 2002 Bacteriorhodopsin similarity (8) #158 - Feb 2013 Proton-Gated Urea Channel similarity (8) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (7) #190 - Oct 2015 Two-component Systems similarity (4) #144 - Dec 2011 Complex I similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#27 - Mar 2002
Bacteriorhodopsin
similarity (8)
#158 - Feb 2013
Proton-Gated Urea Channel
similarity (8)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (7)
#190 - Oct 2015
Two-component Systems
similarity (4)
#144 - Dec 2011
Complex I
similarity (1)
#147 - Mar 2012
Rhodopsin
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)

Deposited unit

A: Sensory rhodopsin-2

B: Sensory rhodopsin II transducer

C: Sensory rhodopsin-2

D: Sensory rhodopsin II transducer

hetero molecules

88.2 kDa, 4 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)	47.131, 109.096, 121.818
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 2 types, 4 molecules ACBD

#1: Protein	Sensory rhodopsin-2 / Sensory rhodopsin II / SR-II Mass: 26534.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Production host: Escherichia coli (E. coli) / References: UniProt: P42196
#2: Protein	Sensory rhodopsin II transducer / HTR-II / Methyl-accepting phototaxis protein II / MPP-II Mass: 14854.804 Da / Num. of mol.: 2 / Mutation: G83F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: htr2, htrII / Production host: Escherichia coli (E. coli) / References: UniProt: P42259

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Sugars , 1 types, 2 molecules

#4: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

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Non-polymers , 3 types, 110 molecules

#3: Chemical	ChemComp-LFA / EICOSANE / LIPID FRAGMENT Mass: 282.547 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₂₀H₄₂
#5: Chemical	ChemComp-RET / RETINAL Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₈O
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.89 Å³/Da / Density % sol: 34.98 %
Crystal grow	Temperature: 293 K / Method: lipidic cubic phase / Details: 1 M Na/K phosphate pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.25→38.055 Å / Num. obs: 30445 / % possible obs: 99.5 % / Redundancy: 3.5 % / R_merge(I) obs: 0.123 / Net I/σ(I): 14.3
Reflection shell	Resolution: 2.25→2.37 Å / R_merge(I) obs: 0.501

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
iMOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1HS2

1hs2

Resolution: 2.25→38.055 Å / Cross valid method: FREE R-VALUE / σ(F): 2

	R_factor	Num. reflection	% reflection
R_free	0.2313	1523	5 %
R_work	0.1861	-	-
obs	0.1883	30445	99.47 %

Refinement step

Cycle: LAST / Resolution: 2.25→38.055 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4139	0	250	93	4482

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4467
X-RAY DIFFRACTION	f_angle_d	1.08	6036
X-RAY DIFFRACTION	f_dihedral_angle_d	13.542	1595
X-RAY DIFFRACTION	f_chiral_restr	0.243	719
X-RAY DIFFRACTION	f_plane_restr	0.004	712

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 (%)
2.2501-2.3227	0.2868	135	0.27	2569	X-RAY DIFFRACTION	100
2.3227-2.4057	0.2914	137	0.2146	2601	X-RAY DIFFRACTION	100
2.4057-2.502	0.2535	137	0.1939	2591	X-RAY DIFFRACTION	100
2.502-2.6158	0.2217	138	0.1656	2621	X-RAY DIFFRACTION	100
2.6158-2.7537	0.2008	137	0.1585	2591	X-RAY DIFFRACTION	100
2.7537-2.9262	0.2156	138	0.1485	2620	X-RAY DIFFRACTION	100
2.9262-3.152	0.2078	140	0.1663	2632	X-RAY DIFFRACTION	100
3.152-3.469	0.2353	137	0.1716	2613	X-RAY DIFFRACTION	100
3.469-3.9705	0.2404	140	0.1859	2673	X-RAY DIFFRACTION	100
3.9705-5.0007	0.2199	141	0.1702	2669	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	2.1202	0.389	-0.2317	5.6498	0.0095	1.9359	0.2242	-0.0988	-0.055	0.6341	-0.2851	0.6347	-0.033	-0.3044	0.0522	0.1795	-0.0375	0.0309	0.3574	0.0273	0.2628	49.8295	2.3089	13.9483
2	2.5949	0.7517	0.7754	4.2707	-4.1267	4.8845	0.5083	0.265	1.9544	0.3244	0.058	1.4199	-1.583	-0.4725	-0.4471	0.5533	0.2272	0.1016	0.5733	0.0277	0.722	46.8587	24.0716	7.3605
3	1.4035	-0.2244	0.5686	5.3386	1.324	1.8124	-0.0291	-0.0381	0.0047	-0.6052	0.0209	0.2406	0.0304	-0.1613	-0.0186	0.1771	0.009	0.0126	0.2517	0.0174	0.2263	54.2468	1.0693	5.524
4	0.4591	0.1969	-0.2601	8.9621	1.0016	1.1716	-0.0128	-0.0503	0.0234	0.3037	0.1447	0.4912	0.055	-0.0703	-0.1167	0.2429	0.0232	0.0178	0.2894	0.0188	0.2475	61.5612	4.2099	3.6492
5	1.2268	-2.0407	0.2686	2.8948	-0.3785	1.0476	0.002	0.1268	0.0392	-0.246	-0.0238	-0.2045	0.1055	0.2004	0.0305	0.2096	-0.0241	0.0222	0.269	-0.0058	0.249	72.0407	4.6666	-0.3467
6	4.2975	-5.3757	-1.6939	6.6531	2.5995	6.4273	-0.3595	0.8283	0.9569	-0.1634	0.066	-0.4906	-0.3582	0.2434	0.2911	0.3531	-0.0573	-0.0098	0.3285	-0.0447	0.5348	70.2239	26.0109	5.1581
7	1.2268	-2.1989	0.2885	8.1949	-2.1254	1.1702	-0.1486	-0.24	0.146	0.5341	0.169	-0.5979	-0.0021	0.1286	-0.0264	0.1644	-0.0091	-0.0195	0.2861	-0.0347	0.1893	69.2864	6.0684	12.2956
8	2.7205	-0.5354	0.0971	9.3554	-0.1022	1.7428	-0.0052	-0.0519	0.3756	0.4409	0.0645	-0.1313	-0.2681	-0.0993	-0.0661	0.2789	0.0198	-0.004	0.2633	0.0032	0.2225	58.279	12.3037	14.8682
9	2.8302	-1.0163	0.1732	2.3399	2.4465	4.2112	0.079	0.0646	-0.1333	0.9108	-0.3486	1.2304	0.0949	-1.1401	0.2413	0.4059	0.0415	0.0286	0.4439	0.0129	0.2716	62.4083	-7.5183	27.3535
10	2.3602	-1.4168	0.4033	9.8754	-1.8354	4.022	-0.1942	-0.0254	0.0354	0.483	0.3059	-0.1424	-0.2312	0.1285	-0.0778	0.3421	0.0554	-0.0318	0.3845	-0.0335	0.1992	70.0606	-2.9145	23.0587
11	2.3925	0.4451	0.2012	4.2381	0.6198	2.1413	0.0671	0.1424	0.2179	0.6319	0.1333	0.2362	0.0752	0.5895	-0.1882	0.1772	-0.0137	0.0446	0.3624	-0.0021	0.201	91.5644	1.5318	42.1687
12	6.3792	-5.0168	-4.4026	3.9583	3.3885	5.4458	0.4534	-0.7684	1.7142	-0.6947	-0.0109	-0.9942	-1.6403	0.3863	-0.3656	0.7709	-0.3446	0.0804	0.8077	0.049	1.0871	94.496	23.237	48.7963
13	1.9799	-1.9926	0.0984	8.884	-0.3598	1.8025	0.0362	0.1495	0.229	-0.0413	-0.2373	-0.1255	-0.3108	0.2479	0.2205	0.2347	-0.0973	-0.016	0.3821	0.0161	0.2861	88.9687	7.0819	50.0888
14	0.6618	-0.801	0.115	2.4092	-0.0528	1.3446	-0.1001	0.1075	-0.1263	0.0617	0.0801	0.2262	0.1575	0.1668	0.0341	0.2593	-0.0189	-0.0159	0.2514	-0.0113	0.2605	80.4126	-1.2867	52.2455
15	0.5747	0.6137	0.2233	2.4215	0.0524	2.2108	-0.0562	0.0279	0.0357	0.0564	-0.0197	0.1865	-0.0266	-0.0419	0.0836	0.1712	-0.0085	0.0061	0.2175	0.0023	0.2353	69.3765	4.0082	56.432
16	7.712	6.0398	-0.8551	5.4255	-2.1506	3.5029	-0.4298	-0.2568	1.4114	0.0106	-0.1778	0.3208	-1.254	-0.4191	0.2678	0.6695	0.0347	-0.1292	0.2243	0.0168	0.5045	71.0492	25.2877	51.0554
17	1.4487	1.5747	0.9557	7.7824	2.2909	1.7015	-0.2598	0.2614	0.3888	-0.7869	0.1954	0.9907	-0.2092	-0.0881	0.0885	0.2337	-0.0153	-0.0191	0.2848	0.04	0.208	72.1063	5.5513	43.781
18	2.322	1.585	-0.6187	6.9845	2.2603	1.1347	-0.1632	0.095	0.0098	-0.7248	0.1098	0.0047	-0.0402	0.0401	0.0566	0.3364	-0.0701	-0.0169	0.3598	0.0263	0.1894	81.8768	5.4315	40.7062
19	2.6924	-0.6709	0.3714	2.7733	-1.8314	6.0867	0.4876	0.2551	-0.2604	1.0578	-0.8456	-0.2812	0.1886	1.0439	0.2848	0.3123	0.0156	-0.0268	0.5793	-0.0264	0.3302	78.9717	-7.8914	28.5361
20	2.89	0.9279	1.6448	7.1326	1.9102	3.0641	-0.1966	0.2231	0.0598	-0.2546	0.136	0.0391	-0.3122	0.1594	0.0251	0.3587	-0.0256	-0.0444	0.3668	0.0412	0.1589	71.3269	-3.3246	32.8822

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 91 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 92 through 142 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 143 through 153 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 154 through 189 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 190 through 225 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 23 through 52 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 53 through 83 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 25 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 26 through 33 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 34 through 55 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 56 through 91 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 92 through 142 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 143 through 153 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 154 through 189 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 190 through 217 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 23 through 52 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 53 through 83 )

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