7ZCM | pdb_00007zcm

Dark state structure of Sensory Rhodopsin II in complex with HtrII solved by room temperature serial synchrotron crystallography

PDB DOI: https://doi.org/10.2210/pdb7ZCM/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Natronomonas pharaonis
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2022-03-28 Released: 2023-11-29
Deposition Author(s): Ortolani, G., Bosman, R., Ostojic, L.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission, Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.350 (Depositor), 0.357 (DCC)
R-Value Work:
0.297 (Depositor), 0.307 (DCC)
R-Value Observed:
0.302 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZCM

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Serial synchrotron crystallography structure of the Sensory rhodopsin II transducer complex

Ortolani, G., Bosman, R., Ostojic, L., Branden, G., Neutze, R.

To be published.

Macromolecule Content

Total Structure Weight: 30.69 kDa
Atom Count: 2,147
Modeled Residue Count: 287
Deposited Residue Count: 291
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory rhodopsin-2	A	225	Natronomonas pharaonis	Mutation(s): 0 Gene Names: sop2, sopII Membrane Entity: Yes
UniProt
Find proteins for P42196 (Natronomonas pharaonis) Explore P42196 Go to UniProtKB: P42196
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42196
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory rhodopsin II transducer	B	66	Natronomonas pharaonis	Mutation(s): 0 Gene Names: htr2, htrII Membrane Entity: Yes
UniProt
Find proteins for P42259 (Natronomonas pharaonis) Explore P42259 Go to UniProtKB: P42259
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42259
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET (Subject of Investigation/LOI) Query on RET Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.350 (Depositor), 0.357 (DCC)
R-Value Work: 0.297 (Depositor), 0.307 (DCC)
R-Value Observed: 0.302 (Depositor)

Space Group: P 2₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.87	α = 90
b = 67.65	β = 90
c = 114.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
careless	data reduction
careless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	X-Probe
Swedish Research Council	Sweden	2015-00560

Revision History (Full details and data files)

Version 1.0: 2023-11-29
Type: Initial release
Version 1.1: 2024-10-09
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.