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  PDBTMMemProtMD


• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.350 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.297 (Depositor), 0.310 (DCC) 
• R-Value Observed: 
  0.302 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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

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 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET (Subject of Investigation/LOI)	C [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.350 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.297 (Depositor), 0.310 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Ortolani, G., Bosman, R., Ostojic, L.

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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  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Structure summary