5NV3

Structure of Rubisco from Rhodobacter sphaeroides in complex with CABP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of Enzyme Repair by the AAA(+) Chaperone Rubisco Activase.

Bhat, J.Y.Milicic, G.Thieulin-Pardo, G.Bracher, A.Maxwell, A.Ciniawsky, S.Mueller-Cajar, O.Engen, J.R.Hartl, F.U.Wendler, P.Hayer-Hartl, M.

(2017) Mol Cell 67: 744-756.e6

  • DOI: https://doi.org/10.1016/j.molcel.2017.07.004
  • Primary Citation of Related Structures:  
    5NV3

  • PubMed Abstract: 

    How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.


  • 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 large chain467Cereibacter sphaeroidesMutation(s): 0 
Gene Names: cbbLcbbL1rbcL
EC: 4.1.1.39
UniProt
Find proteins for P27997 (Cereibacter sphaeroides)
Explore P27997 
Go to UniProtKB:  P27997
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27997
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small chain 1129Cereibacter sphaeroidesMutation(s): 0 
Gene Names: cbbSrbcS
EC: 4.1.1.39
UniProt
Find proteins for P27998 (Cereibacter sphaeroides)
Explore P27998 
Go to UniProtKB:  P27998
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27998
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
Q [auth A]
S [auth B]
AA [auth F],
CA [auth G],
EA [auth H],
Q [auth A],
S [auth B],
U [auth C],
W [auth D],
Y [auth E]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth G]
FA [auth H]
R [auth A]
T [auth B]
BA [auth F],
DA [auth G],
FA [auth H],
R [auth A],
T [auth B],
V [auth C],
X [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
C [auth B]
E [auth C]
G [auth D]
I [auth E]
A,
C [auth B],
E [auth C],
G [auth D],
I [auth E],
K [auth F],
M [auth G],
O [auth H]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0155
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Database references, Refinement description
  • Version 1.2: 2017-09-20
    Changes: Database references