[English] 日本語
Yorodumi
- PDB-2f95: M intermediate structure of sensory rhodopsin II/transducer compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f95
TitleM 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 / MEMBRANE 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: 2.2 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.G. / Granzin, J. / Schlesinger, R. / Bueldt, G. / Savapol, T. / Scheidig, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensory rhodopsin II
B: Sensory rhodopsin II transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3364
Polymers43,7592
Non-polymers5772
Water59433
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)88,6728
Polymers87,5184
Non-polymers1,1544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6290 Å2
ΔGint-63 kcal/mol
Surface area23420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.620, 46.900, 53.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Number of models2
DetailsBiological unit is thought to consist of one ground state complex of sensory rhodopsin II/transducer and one M state complex which is positioned relative to ground state by application of two fold operator: 1-x, -y, z

-
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: 17224.270 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.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.6 %
Crystal growTemperature: 296 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 296K

-
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: 2.2→22.01 Å / Num. all: 16493 / Num. obs: 16147 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 3.9 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.414 / % possible all: 99.4

-
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: 2.2→22.01 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2058714.26 / 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 M 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 M 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 M STATE MODEL WAS REFINED WITH GROUND STATE MODEL FIXED AGAINST THE ILLUMINATED CRYSTAL DATA
RfactorNum. reflection% reflectionSelection details
Rfree0.241 767 4.9 %RANDOM
Rwork0.217 ---
all0.219 16147 --
obs0.217 15688 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.764 Å2 / ksol: 0.347059 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.38 Å20 Å20 Å2
2---0.25 Å20 Å2
3----4.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 40 33 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.32.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 74 4.8 %
Rwork0.24 1466 -
obs--94.3 %
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more