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

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Basic information

Entry
Database: PDB / ID: 5jjn
TitleStructure of the SRII/HtrII(G83F) Complex in P212121 space group ("V" shape)
Components
  • Sensory rhodopsin II transducer
  • Sensory rhodopsin-2
KeywordsSIGNALING PROTEIN / sensory rhodopsin II / transducer / membrane protein complex
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Htr2, transmembrane domain / Htr2 transmembrane domain / Helix hairpin bin / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...Htr2, transmembrane domain / Htr2 transmembrane domain / Helix hairpin bin / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / Bacterial rhodopsins retinal binding site. / HAMP domain profile. / HAMP domain / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EICOSANE / RETINAL / Sensory rhodopsin-2 / Sensory rhodopsin II transducer
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsIshchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J. / Remeeva, A. / Polovinkin, V. / Utrobin, P. / Balandin, T. ...Ishchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J. / Remeeva, A. / Polovinkin, V. / Utrobin, P. / Balandin, T. / Engelhard, M. / Bueldt, G. / Gordeliy, V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RSF14-14-00995 Russian Federation
CitationJournal: 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
DepositionApr 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: 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 1.2Jan 10, 2024Group: 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
C: Sensory rhodopsin-2
D: Sensory rhodopsin II transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,17123
Polymers82,7794
Non-polymers5,39219
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-23 kcal/mol
Surface area23790 Å2
MethodPISA
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 number19
Space group name H-MP212121

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Components

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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
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.25→38.055 Å / Num. obs: 30445 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 14.3
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.501

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HS2

1hs2


Resolution: 2.25→38.055 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.2313 1523 5 %
Rwork0.1861 --
obs0.1883 30445 99.47 %
Refinement stepCycle: LAST / Resolution: 2.25→38.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 250 93 4482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014467
X-RAY DIFFRACTIONf_angle_d1.086036
X-RAY DIFFRACTIONf_dihedral_angle_d13.5421595
X-RAY DIFFRACTIONf_chiral_restr0.243719
X-RAY DIFFRACTIONf_plane_restr0.004712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.32270.28681350.272569X-RAY DIFFRACTION100
2.3227-2.40570.29141370.21462601X-RAY DIFFRACTION100
2.4057-2.5020.25351370.19392591X-RAY DIFFRACTION100
2.502-2.61580.22171380.16562621X-RAY DIFFRACTION100
2.6158-2.75370.20081370.15852591X-RAY DIFFRACTION100
2.7537-2.92620.21561380.14852620X-RAY DIFFRACTION100
2.9262-3.1520.20781400.16632632X-RAY DIFFRACTION100
3.152-3.4690.23531370.17162613X-RAY DIFFRACTION100
3.469-3.97050.24041400.18592673X-RAY DIFFRACTION100
3.9705-5.00070.21991410.17022669X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.12020.389-0.23175.64980.00951.93590.2242-0.0988-0.0550.6341-0.28510.6347-0.033-0.30440.05220.1795-0.03750.03090.35740.02730.262849.82952.308913.9483
22.59490.75170.77544.2707-4.12674.88450.50830.2651.95440.32440.0581.4199-1.583-0.4725-0.44710.55330.22720.10160.57330.02770.72246.858724.07167.3605
31.4035-0.22440.56865.33861.3241.8124-0.0291-0.03810.0047-0.60520.02090.24060.0304-0.1613-0.01860.17710.0090.01260.25170.01740.226354.24681.06935.524
40.45910.1969-0.26018.96211.00161.1716-0.0128-0.05030.02340.30370.14470.49120.055-0.0703-0.11670.24290.02320.01780.28940.01880.247561.56124.20993.6492
51.2268-2.04070.26862.8948-0.37851.04760.0020.12680.0392-0.246-0.0238-0.20450.10550.20040.03050.2096-0.02410.02220.269-0.00580.24972.04074.6666-0.3467
64.2975-5.3757-1.69396.65312.59956.4273-0.35950.82830.9569-0.16340.066-0.4906-0.35820.24340.29110.3531-0.0573-0.00980.3285-0.04470.534870.223926.01095.1581
71.2268-2.19890.28858.1949-2.12541.1702-0.1486-0.240.1460.53410.169-0.5979-0.00210.1286-0.02640.1644-0.0091-0.01950.2861-0.03470.189369.28646.068412.2956
82.7205-0.53540.09719.3554-0.10221.7428-0.0052-0.05190.37560.44090.0645-0.1313-0.2681-0.0993-0.06610.27890.0198-0.0040.26330.00320.222558.27912.303714.8682
92.8302-1.01630.17322.33992.44654.21120.0790.0646-0.13330.9108-0.34861.23040.0949-1.14010.24130.40590.04150.02860.44390.01290.271662.4083-7.518327.3535
102.3602-1.41680.40339.8754-1.83544.022-0.1942-0.02540.03540.4830.3059-0.1424-0.23120.1285-0.07780.34210.0554-0.03180.3845-0.03350.199270.0606-2.914523.0587
112.39250.44510.20124.23810.61982.14130.06710.14240.21790.63190.13330.23620.07520.5895-0.18820.1772-0.01370.04460.3624-0.00210.20191.56441.531842.1687
126.3792-5.0168-4.40263.95833.38855.44580.4534-0.76841.7142-0.6947-0.0109-0.9942-1.64030.3863-0.36560.7709-0.34460.08040.80770.0491.087194.49623.23748.7963
131.9799-1.99260.09848.884-0.35981.80250.03620.14950.229-0.0413-0.2373-0.1255-0.31080.24790.22050.2347-0.0973-0.0160.38210.01610.286188.96877.081950.0888
140.6618-0.8010.1152.4092-0.05281.3446-0.10010.1075-0.12630.06170.08010.22620.15750.16680.03410.2593-0.0189-0.01590.2514-0.01130.260580.4126-1.286752.2455
150.57470.61370.22332.42150.05242.2108-0.05620.02790.03570.0564-0.01970.1865-0.0266-0.04190.08360.1712-0.00850.00610.21750.00230.235369.37654.008256.432
167.7126.0398-0.85515.4255-2.15063.5029-0.4298-0.25681.41140.0106-0.17780.3208-1.254-0.41910.26780.66950.0347-0.12920.22430.01680.504571.049225.287751.0554
171.44871.57470.95577.78242.29091.7015-0.25980.26140.3888-0.78690.19540.9907-0.2092-0.08810.08850.2337-0.0153-0.01910.28480.040.20872.10635.551343.781
182.3221.585-0.61876.98452.26031.1347-0.16320.0950.0098-0.72480.10980.0047-0.04020.04010.05660.3364-0.0701-0.01690.35980.02630.189481.87685.431540.7062
192.6924-0.67090.37142.7733-1.83146.08670.48760.2551-0.26041.0578-0.8456-0.28120.18861.04390.28480.31230.0156-0.02680.5793-0.02640.330278.9717-7.891428.5361
202.890.92791.64487.13261.91023.0641-0.19660.22310.0598-0.25460.1360.0391-0.31220.15940.02510.3587-0.0256-0.04440.36680.04120.158971.3269-3.324632.8822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 142 )
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 153 )
7X-RAY DIFFRACTION7chain 'A' and (resid 154 through 189 )
8X-RAY DIFFRACTION8chain 'A' and (resid 190 through 225 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 83 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 25 )
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 33 )
13X-RAY DIFFRACTION13chain 'C' and (resid 34 through 55 )
14X-RAY DIFFRACTION14chain 'C' and (resid 56 through 91 )
15X-RAY DIFFRACTION15chain 'C' and (resid 92 through 142 )
16X-RAY DIFFRACTION16chain 'C' and (resid 143 through 153 )
17X-RAY DIFFRACTION17chain 'C' and (resid 154 through 189 )
18X-RAY DIFFRACTION18chain 'C' and (resid 190 through 217 )
19X-RAY DIFFRACTION19chain 'D' and (resid 23 through 52 )
20X-RAY DIFFRACTION20chain 'D' and (resid 53 through 83 )

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