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- PDB-1h2s: Molecular basis of transmenbrane signalling by sensory rhodopsin ... -

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Basic information

Entry
Database: PDB / ID: 1h2s
TitleMolecular basis of transmenbrane signalling by sensory rhodopsin II-transducer complex
Components
  • SENSORY RHODOPSIN II
  • SENSORY RHODOPSIN II TRANSDUCER
KeywordsMEMBRANE PROTEIN / MENBRANE PROTEIN COMPLEX / SIGNAL TRANSDUCTION
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
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
RETINAL / Sensory rhodopsin-2 / Sensory rhodopsin II transducer
Similarity search - Component
Biological speciesNATRONOMONAS PHARAONIS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGordeliy, V.I. / Labahn, J. / Moukhametzianov, R. / Efremov, R. / Granzin, J. / Schlesinger, R. / Bueldt, G. / Savopol, T. / Scheidig, A. / Klare, J.P. / Engelhard, M.
CitationJournal: Nature / Year: 2002
Title: Molecular Basis of Transmembrane Signalling by Sensory Rhodopsin II-Transducer Complex
Authors: Gordeliy, V.I. / Labahn, J. / Moukhametzianov, R. / Efremov, R. / Granzin, J. / Schlesinger, R. / Bueldt, G. / Savopol, T. / Scheidig, A. / Klare, J.P. / Engelhard, M.
History
DepositionAug 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_validate_close_contact / struct_biol / struct_conn
Item: _exptl_crystal_grow.method
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _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 II
B: SENSORY RHODOPSIN II TRANSDUCER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3774
Polymers29,8002
Non-polymers5772
Water72140
1
A: SENSORY RHODOPSIN II
B: SENSORY RHODOPSIN II TRANSDUCER
hetero molecules

A: SENSORY RHODOPSIN II
B: SENSORY RHODOPSIN II TRANSDUCER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7548
Polymers59,6004
Non-polymers1,1544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.300, 46.960, 53.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SENSORY RHODOPSIN II


Mass: 24085.465 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-225
Source method: isolated from a genetically manipulated source
Details: HIS-TAG / Source: (gene. exp.) NATRONOMONAS PHARAONIS (archaea) / Plasmid: PET27BMOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42196
#2: Protein SENSORY RHODOPSIN II TRANSDUCER / TRANSDUCER HTR II FRAGMENT / HTR-II / METHYL-ACCEPTING PHOTOTAXIS PROTEIN II / MPP-II


Mass: 5714.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-82
Source method: isolated from a genetically manipulated source
Details: HIS-TAG / Source: (gene. exp.) NATRONOMONAS PHARAONIS (archaea) / Plasmid: PET27BMOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42259
#3: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSENSORY RHODOPSIN II INVOLVED IN CONTROL OF PHOTOTAXIS. SEEMS TO ACTIVATE A METHYL-ACCEPTING ...SENSORY RHODOPSIN II INVOLVED IN CONTROL OF PHOTOTAXIS. SEEMS TO ACTIVATE A METHYL-ACCEPTING PROTEIN (HTR-II). SENSORY RHODOPSIN II TRANSDUCER (HTR-II) TRANSDUCES SIGNALS FROM THE PHOTOTAXIS RECEPTOR SENSORY RHODOPSIN II TO FLAGELLAR MOTOR.

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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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 5.1
Details: 150 MM NACL, 25 MM NAKPI 5.1 0.8% B-OCTYLGLUCOSID , MONOVACCENIN (CUBIC PHASE) PRECIPITATED BY 1 M NA/KPI 5.8 AT 22 C, pH 5.10
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1150 mM11NaCl
225 mMsodium potassium Pi11pH5.1
30.8 %n-octyl-beta-D-glucopyranoside11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.93→60 Å / Num. obs: 23156 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 5.5
Reflection shell
*PLUS
% possible obs: 77.3 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JGJ

1jgj


Resolution: 1.93→60 Å / Data cutoff high absF: 1000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 1143 4.7 %RANDOM
Rwork0.2255 ---
obs0.2255 23156 94.7 %-
Solvent computationSolvent model: FLAT
Displacement parametersBiso mean: 32.3815 Å2
Baniso -1Baniso -2Baniso -3
1--2.111 Å20 Å20 Å2
2---1.799 Å20 Å2
3---3.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati sigma a0.14 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.93→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 40 40 2187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009247
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.07126
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.98526
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79506
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.93→2 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.272 77
Rwork0.2352 1765
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.LINKPROTEIN.TOP
X-RAY DIFFRACTION2PROTEIN_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION4BOG.PARAMBOG.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.98526
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79506

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