5Z49

Crystal structure of the effector-binding domain of Synechococcus elongatus CmpR in complex with ribulose-1,5-bisphosphate

• PDB DOI: https://doi.org/10.2210/pdb5Z49/pdb

• Classification: TRANSCRIPTION
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-10 Released: 2018-10-10 
• Deposition Author(s): Jiang, Y.L., Mahounga, D.M., Sun, H.
• Funding Organization(s): National Natural Science Foundation of China

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.241 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Crystal structure of the effector-binding domain of Synechococcus elongatus CmpR in complex with ribulose 1,5-bisphosphate.

Mahounga, D.M., Sun, H., Jiang, Y.L.

(2018) Acta Crystallogr F Struct Biol Commun 74: 506-511

• PubMed: 30084400 
• DOI: https://doi.org/10.1107/S2053230X18008841
• Primary Citation of Related Structures:  
  5Z49


• PubMed Abstract: 
  

  The CO ₂ -concentrating mechanism (CCM) has evolved to improve the efficiency of photosynthesis in autotrophic cyanobacteria. CmpR, a LysR-type transcriptional regulator (LTTR) from Synechococcus elongatus PCC 7942, was found to regulate CCM-related genes under low-CO ₂ conditions. Here, the dimeric structure of the effector-binding domain of CmpR (CmpR-EBD) in complex with the co-activator ribulose 1,5-bisphosphate (RuBP) is reported at 2.15 Å resolution. One RuBP molecule binds to the inter-domain cleft between the two subunits of the CmpR-EBD dimer. Structural comparison combined with sequence analyses demonstrated that CmpR-EBD has an overall structure similar to those of LTTRs of known structure, but possesses a distinctly different effector-binding pattern.

---

Organizational Affiliation: 

School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.88 kDa 
• Atom Count: 3,643 
• Modelled Residue Count: 440 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional activator CmpR	A [auth B], B [auth A]	239	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0  Gene Names: cmpR, Synpcc7942_1310
UniProt
Find proteins for Q9F1R2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q9F1R2  Go to UniProtKB:  Q9F1R2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RUB	C [auth A]	RIBULOSE-1,5-DIPHOSPHATE C5 H12 O11 P2 YAHZABJORDUQGO-NQXXGFSBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.241 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.57	α = 90
b = 86.7	β = 90
c = 87.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Jiang, Y.L., Mahounga, D.M., Sun, H.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31630001
National Natural Science Foundation of China	China	31500598

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary