PDBsum entry: 2f95

Membrane protein

PDB-id: 2f95

Asymmetric unit

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Description

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Header records

References

PROCHECK

Protein chains

220 a.a. *

53 a.a. *

Ligands

BOG

RET

Waters ×33

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, tetramer
- as defined in PDB file (see also PQS)

PDB id:

2f95

Name:

Membrane protein

Title:

M intermediate structure of sensory rhodopsin ii/transducer complex in combination with the ground state structure

Structure:

Sensory rhodopsin ii. Chain: a. Synonym: sr-ii. Engineered: yes. Sensory rhodopsin ii transducer. Chain: b. Synonym: htr-ii, methyl-accepting phototaxis protein ii, mpp-ii. Engineered: yes

Source:

Natronomonas pharaonis. Organism_taxid: 2257. Gene: sop2, sopii. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: htr2, htrii.

Biological unit:

Tetramer (from PDB file)

UniProt:

Chain A: P42196 (BACS2_NATPH)

Seq:	239 a.a.
Struc:	220 a.a.

Chain B: P42259 (HTR2_NATPH)

Seq:

Struc:

Seq:

Struc:

Seq:

534 a.a.

Struc:

53 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

Resolution:

2.20Å

R-factor:

0.217

R-free:

0.241

Authors:

R.I.Moukhametzianov,J.P.Klare,R.G.Efremov,C.Baecken, A.Goeppner,J.Labahn,M.Engelhard,G.Bueldt,V.I.Gordeliy

Key ref:

R.Moukhametzianov et al. (2006). Development of the signal in sensory rhodopsin and its transfer to the cognate transducer.. Nature, 440, 115-119. [PubMed id: 16452929] [DOI: 10.1038/nature04520]

Date:

05-Dec-05

Release date:

07-Mar-06

Related entries:

2f93
k state of sensory rhodopsin ii/transducer complex
1h2s
ground state of sensory rhodopsin ii/transducer complex

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Clefts

Surface

Key reference

DOI no: 10.1038/nature04520

Nature 440:115-119 (2006)

PubMed id: 16452929

Development of the signal in sensory rhodopsin and its transfer to the cognate transducer.

R.Moukhametzianov, J.P.Klare, R.Efremov, C.Baeken, A.Göppner, J.Labahn, M.Engelhard, G.Büldt, V.I.Gordeliy.

ABSTRACT

The microbial phototaxis receptor sensory rhodopsin II (NpSRII, also named phoborhodopsin) mediates the photophobic response of the haloarchaeon Natronomonas pharaonis by modulating the swimming behaviour of the bacterium. After excitation by blue-green light NpSRII triggers, by means of a tightly bound transducer protein (NpHtrII), a signal transduction chain homologous with the two-component system of eubacterial chemotaxis. Two molecules of NpSRII and two molecules of NpHtrII form a 2:2 complex in membranes as shown by electron paramagnetic resonance and X-ray structure analysis. Here we present X-ray structures of the photocycle intermediates K and late M (M2) explaining the evolution of the signal in the receptor after retinal isomerization and the transfer of the signal to the transducer in the complex. The formation of late M has been correlated with the formation of the signalling state. The observed structural rearrangements allow us to propose the following mechanism for the light-induced activation of the signalling complex. On excitation by light, retinal isomerization leads in the K state to a rearrangement of a water cluster that partly disconnects two helices of the receptor. In the transition to late M the changes in the hydrogen bond network proceed further. Thus, in late M state an altered tertiary structure establishes the signalling state of the receptor. The transducer responds to the activation of the receptor by a clockwise rotation of about 15 degrees of helix TM2 and a displacement of this helix by 0.9 A at the cytoplasmic surface.

Selected figure(s)

Figure 2.
Figure 2: Structural changes in the extracellular vicinity of the retinal Schiff base. Hydrogen-bond pattern including four water molecules, Lys 205, Asp 75, Asp 201, Arg 72 and Thr 79 side chains, showing ground state (red), intermediate states (yellow), water molecules of ground state (red balls) and intermediate states (yellow balls). Hydrogen bonds are shown as red dotted lines for the ground state and as black dotted lines for the intermediate states. Difference densities are shown in blue for negative densities and red for positive densities (Methods). a, K state of complex with electron density maps contoured at 4.5 and -4.5 . b, M intermediate of complex with electron density maps contoured at 3 and -3 . c, Analogue residues of ground-state and late M-state structures of bacteriorhodopsin (Protein Data Bank accession code 1CWQ).

Figure 4.
Figure 4: Overall views of helices F, G, TM1 and TM2 in ground and late M states. a, Structural changes along these helices; colours are as in Fig. 3c. b, Schematic picture of helical displacements viewed from the cytoplasmic surface. The ground-state complex is shown in red and the late M-state complex in yellow; black numbers give distances between C atoms of the following amino acids in the ground and late M states: F(Leu 170) to TM2(Leu 77), ground state 7.4 Å, M state 8.0 Å; G(Val 203) to TM2(Leu 77), ground state 8.3 Å, M state 7.8 Å; TM2(Val 78) to TM2'(Val 78), ground state 12.0 Å, M state 12.3 Å. The arrows on TM1 and TM2 depict displacements parallel to the membrane plane in late M; the thick arrow on helix G depicts its 0.5 Å movement to the extracellular side. A clockwise rotation of 15° is observed for TM2 and an in-plane displacement of 0.9 Å (black arrow) near the cytoplasmic membrane surface in late M state with respect to the ground state. A red line in the receptor coloured yellow divides the molecule into the two functionally important domains ABG and CDEF. The inner red shaded circles of helices A, B and G depict their movements to the extracellular side.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 440, 115-119) copyright 2006.

Figures were selected by the author.