Macromolecule Content

Total Structure Weight: 42.94 kDa
Atom Count: 2904
Modelled Residue Count: 337
Deposited Residue Count: 359
Unique protein chains: 2

3PQR

Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin

DOI: 10.2210/pdb3PQR/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bos taurus
Mutation(s): Yes

Deposited: 2010-11-26 Released: 2011-03-09
Deposition Author(s): Choe, H.-W., Kim, Y.J., Park, J.H., Morizumi, T., Pai, E.F., Krauss, N., Hofmann, K.P., Scheerer, P., Ernst, O.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.250
R-Value Work: 0.217

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of metarhodopsin II.

Choe, H.W., Kim, Y.J., Park, J.H., Morizumi, T., Pai, E.F., Krauss, N., Hofmann, K.P., Scheerer, P., Ernst, O.P.

(2011) Nature 471: 651-655

PubMed: 21389988 Search on PubMed
DOI: 10.1038/nature09789
Primary Citation of Related Structures:
3PXO, 3PQR

PubMed Abstract:

G-protein-coupled receptors (GPCRs) are seven transmembrane helix (TM) proteins that transduce signals into living cells by binding extracellular ligands and coupling to intracellular heterotrimeric G proteins (Gαβγ). The photoreceptor rhodopsin couples to transducin and bears its ligand 11-cis-retinal covalently bound via a protonated Schiff base to the opsin apoprotein. Absorption of a photon causes retinal cis/trans isomerization and generates the agonist all-trans-retinal in situ. After early photoproducts, the active G-protein-binding intermediate metarhodopsin II (Meta II) is formed, in which the retinal Schiff base is still intact but deprotonated. Dissociation of the proton from the Schiff base breaks a major constraint in the protein and enables further activating steps, including an outward tilt of TM6 and formation of a large cytoplasmic crevice for uptake of the interacting C terminus of the Gα subunit. Owing to Schiff base hydrolysis, Meta II is short-lived and notoriously difficult to crystallize. We therefore soaked opsin crystals with all-trans-retinal to form Meta II, presuming that the crystal's high concentration of opsin in an active conformation (Ops*) may facilitate all-trans-retinal uptake and Schiff base formation. Here we present the 3.0 Å and 2.85 Å crystal structures, respectively, of Meta II alone or in complex with an 11-amino-acid C-terminal fragment derived from Gα (GαCT2). GαCT2 binds in a large crevice at the cytoplasmic side, akin to the binding of a similar Gα-derived peptide to Ops* (ref. 7). In the Meta II structures, the electron density from the retinal ligand seamlessly continues into the Lys 296 side chain, reflecting proper formation of the Schiff base linkage. The retinal is in a relaxed conformation and almost undistorted compared with pure crystalline all-trans-retinal. By comparison with early photoproducts we propose how retinal translocation and rotation induce the gross conformational changes characteristic for Meta II. The structures can now serve as models for the large GPCR family.

Organizational Affiliation:

Institut für Medizinische Physik und Biophysik - CC2, Charité - Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany. hwchoe@jbnu.ac.kr

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	348	Bos taurus	Mutation(s): 0 Gene Names: RHO
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: G Protein-Coupled Receptors: Class A	Protein: Rhodopsin in Meta II state
Find proteins for P02699 (Bos taurus) Explore P02699 Go to UniProtKB: P02699
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(t) subunit alpha-1	B	11	Bos taurus	Mutation(s): 2 Gene Names: GNAT1
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: G Protein-Coupled Receptors: Class A	Protein: Rhodopsin in Meta II state
Find proteins for P04695 (Bos taurus) Explore P04695 Go to UniProtKB: P04695
Protein Feature View Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation	Oligosaccharides Interaction

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	D	2		N/A	Oligosaccharides Interaction

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	G [auth A], H [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Ligand Interaction
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Ligand Interaction
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Ligand Interaction
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	K [auth A], L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	D	trehalose	Oligosaccharide / Nutrient		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.250
R-Value Work: 0.217
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 241.55	α = 90
b = 241.55	β = 90
c = 109.87	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2010-11-26
Released Date: 2011-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

178747 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

3PQR

Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin

Crystal structure of metarhodopsin II.

Entity ID: 1

Membrane protein

Protein Feature View

Expand

Entity ID: 2