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- PDB-5jjj: Structure of the SRII/HtrII Complex in P64 space group ("U" shape) -

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Basic information

Entry
Database: PDB / ID: 5jjj
TitleStructure of the SRII/HtrII Complex in P64 space group ("U" shape)
Components
  • Sensory rhodopsin II transducer
  • Sensory rhodopsin-2
KeywordsSIGNALING PROTEIN / sensory rhodopsin II / transducer / membrane protein complex
Function / homology
Function and homology information


photoreceptor activity / phototransduction / transmembrane signaling receptor activity / chemotaxis / lysozyme activity / monoatomic ion channel 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: 2.5 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 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,84411
Polymers41,3002
Non-polymers2,5459
Water46826
1
A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules

A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,68922
Polymers82,5994
Non-polymers5,09018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area14040 Å2
ΔGint-23 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.310, 66.310, 170.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Sensory rhodopsin-2 / Sensory rhodopsin II / SR-II


Mass: 26534.941 Da / Num. of mol.: 1
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: 14764.683 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H42
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.94 %
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: 2.5→34 Å / Num. obs: 20997 / % possible obs: 77.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.16
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.396

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HS2

1hs2


Resolution: 2.5→34 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2326 1080 5.14 %
Rwork0.179 --
obs0.1819 20997 72.52 %
Refinement stepCycle: LAST / Resolution: 2.5→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 110 26 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082202
X-RAY DIFFRACTIONf_angle_d1.2922975
X-RAY DIFFRACTIONf_dihedral_angle_d13.624798
X-RAY DIFFRACTIONf_chiral_restr0.061361
X-RAY DIFFRACTIONf_plane_restr0.004345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61380.28081370.21562345X-RAY DIFFRACTION69
2.6138-2.75150.27021280.17992398X-RAY DIFFRACTION69
2.7515-2.92380.2021240.17092386X-RAY DIFFRACTION70
2.9238-3.14940.25521240.16282443X-RAY DIFFRACTION70
3.1494-3.46610.24061270.16492379X-RAY DIFFRACTION70
3.4661-3.9670.24451240.16462441X-RAY DIFFRACTION71
3.967-4.99550.18341610.15222619X-RAY DIFFRACTION77
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)
12.9869-0.80061.39682.67430.34914.45040.05460.144-0.34620.16820.10420.14910.34890.0348-0.12380.222-0.0190.07490.416-0.07770.4782-39.413318.45820.3023
21.4093-0.2124-1.98751.34230.64953.1975-0.08810.05560.10220.12330.09380.0404-0.04370.3318-0.00680.2057-0.008-0.02980.5636-0.00560.3615-36.136631.8892.5127
32.8267-0.5341.10624.4057-2.11132.1796-0.1176-0.4056-0.08340.62990.50940.3680.08750.5263-0.37680.34250.09930.04290.83650.03310.4727-18.636520.0657-10.1197
42.5710.2583-3.93184.1558-0.98117.29660.3095-0.5459-0.18180.27630.35990.1445-1.0129-0.8692-0.67410.3042-0.00990.00850.78260.05640.3221-21.329629.1341-10.5311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 216 )
3X-RAY DIFFRACTION3chain 'B' and (resid 23 through 50 )
4X-RAY DIFFRACTION4chain 'B' and (resid 51 through 82 )

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