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- PDB-2f93: K Intermediate Structure of Sensory Rhodopsin II/Transducer Compl... -

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Basic information

Entry
Database: PDB / ID: 2f93
TitleK Intermediate Structure of Sensory Rhodopsin II/Transducer Complex in Combination with the Ground State Structure
Components
  • Sensory rhodopsin II
  • Sensory rhodopsin II transducer
KeywordsMEMBRANE PROTEIN / MENBRANE PROTEIN COMPLEX / SIGNAL TRANSDUCTION / PHOTOCYCLE STATE
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
RETINAL / Sensory rhodopsin-2 / Sensory rhodopsin II transducer
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMoukhametzianov, R.I. / Klare, J.P. / Efremov, R.G. / Baecken, C. / Goeppner, A. / Labahn, J. / Engelhard, M. / Bueldt, G. / Gordeliy, V.I.
Citation
Journal: Nature / Year: 2006
Title: Development of the signal in sensory rhodopsin and its transfer to the cognate transducer.
Authors: Moukhametzianov, R. / Klare, J.P. / Efremov, R. / Baeken, C. / Goppner, A. / Labahn, J. / Engelhard, M. / Buldt, G. / Gordeliy, V.I.
#1: Journal: Nature / Year: 2002
Title: Molecular basis of transmembrane signalling by sensory rhodopsin II - transducer complex
Authors: Gordeliy, V.I. / Labahn, J. / Moukhametzianov, R.I. / Efremov, R. / Granzin, J. / Schlesinger, R. / Bueldt, G. / Savapol, T. / Schedig, A.J. / Klare, J.P. / Engelhard, M.
History
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)39,6604
Polymers39,0832
Non-polymers5772
Water63135
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)79,3208
Polymers78,1664
Non-polymers1,1544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7490 Å2
ΔGint-49 kcal/mol
Surface area22080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.340, 47.030, 53.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Number of models2
DetailsFunctional K state is thought to consist of one ground state complex of sensory rhoodpsin II/transducer and one K state complex which is to be generated by applying the two fold operator to the K state: 1-x, -y, z

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Components

#1: Protein 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 / Plasmid: PET27BMOD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42196
#2: Protein Sensory rhodopsin II transducer / HTR-II / Methyl-accepting phototaxis protein II / MPP-II


Mass: 12548.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: htr2, htrII / Plasmid: PET27BMOD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 35 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 295 K / pH: 5.8
Details: 150 MM NACL, 25 MM NAKPI 5.1 0.8% B-OCTYLGLUCOSID , MONOVACCENIN (CUBIC PHASE) PRECIPITATED BY 1 M NA/KPI 5.8 , in cubic lipidic phase, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→34.06 Å / Num. all: 22023 / Num. obs: 21010 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 3.8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.091
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.494 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1H2S

1h2s


Resolution: 2→34.06 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1775916.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: MODEL USED FOR REFINEMENT CONSISTS OF GROUND STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR A AT POSITION 17) AND K STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR B AT POSITION 17) ...Details: MODEL USED FOR REFINEMENT CONSISTS OF GROUND STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR A AT POSITION 17) AND K STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR B AT POSITION 17) WITH CORRESPONDING OCCUPANCIES. GROUND STATE MODEL WAS FIRST REFINED AGAINST THE GROUND STATE DATA AND THEN THE K STATE MODEL WAS REFINED WITH GROUND STATE MODEL FIXED AGAINST THE ILLUMINATED CRYSTAL DATA
RfactorNum. reflection% reflectionSelection details
Rfree0.245 985 4.8 %RANDOM
Rwork0.218 ---
all0.219 21010 --
obs0.218 20360 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 94.103 Å2 / ksol: 0.453145 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å20 Å20 Å2
2--2.82 Å20 Å2
3----5.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 40 35 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d16.8
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.239 99 4.9 %
Rwork0.234 1926 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BOG.PARBOG.TOP
X-RAY DIFFRACTION3RETINAL.PARRETINAL.TOP
X-RAY DIFFRACTION4WATER_REP.PARAM

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