[English] 日本語
Yorodumi
- PDB-5jjj: Structure of the SRII/HtrII Complex in P64 space group ("U" shape) -

+
Open data


ID or keywords:

Loading...

-
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


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: 2.5 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
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