6Z1F

CryoEM structure of Rubisco Activase with its substrate Rubisco from Nostoc sp. (strain PCC7120)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes.

Flecken, M.Wang, H.Popilka, L.Hartl, F.U.Bracher, A.Hayer-Hartl, M.

(2020) Cell 183: 457-473.e20

  • DOI: https://doi.org/10.1016/j.cell.2020.09.010
  • Primary Citation of Related Structures:  
    6HAS, 6Z1D, 6Z1E, 6Z1F, 6Z1G

  • PubMed Abstract: 

    Rubisco, the key enzyme of CO 2 fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization.


  • Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase/oxygenase activase290Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: rcaalr1533
UniProt
Find proteins for P58555 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58555 
Go to UniProtKB:  P58555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58555
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain476Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cbbLrbcrbcArbcLalr1524
EC: 4.1.1.39
UniProt
Find proteins for P00879 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P00879 
Go to UniProtKB:  P00879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00879
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small chain109Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cbbSrbcSalr1526
EC: 4.1.1.39
UniProt
Find proteins for P06514 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P06514 
Go to UniProtKB:  P06514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06514
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
BA [auth 4],
DA [auth 5],
FA [auth 6],
X [auth 2],
Z [auth 3]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
W [auth 1]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CAP
Query on CAP

Download Ideal Coordinates CCD File 
HA [auth A]
KA [auth C]
MA [auth D]
OA [auth E]
QA [auth F]
HA [auth A],
KA [auth C],
MA [auth D],
OA [auth E],
QA [auth F],
SA [auth G],
UA [auth H]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 3]
CA [auth 4]
EA [auth 5]
GA [auth A]
IA [auth B]
AA [auth 3],
CA [auth 4],
EA [auth 5],
GA [auth A],
IA [auth B],
JA [auth C],
LA [auth D],
NA [auth E],
PA [auth F],
RA [auth G],
TA [auth H],
Y [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
G [auth A]
H [auth B]
I [auth C]
J [auth D]
K [auth E]
G [auth A],
H [auth B],
I [auth C],
J [auth D],
K [auth E],
L [auth F],
M [auth G],
N [auth H]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0155

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references