6EKC

Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Plant RuBisCo assembly in E. coli with five chloroplast chaperones including BSD2.

Aigner, H., Wilson, R.H., Bracher, A., Calisse, L., Bhat, J.Y., Hartl, F.U., Hayer-Hartl, M.

(2017) Science 358: 1272-1278

  • DOI: https://doi.org/10.1126/science.aap9221
  • Primary Citation of Related Structures:  
    6EKB, 6EKC

  • PubMed Abstract: 

    Plant RuBisCo, a complex of eight large and eight small subunits, catalyzes the fixation of CO 2 in photosynthesis. The low catalytic efficiency of RuBisCo provides strong motivation to reengineer the enzyme with the goal of increasing crop yields. However, genetic manipulation has been hampered by the failure to express plant RuBisCo in a bacterial host. We achieved the functional expression of Arabidopsis thaliana RuBisCo in Escherichia coli by coexpressing multiple chloroplast chaperones. These include the chaperonins Cpn60/Cpn20, RuBisCo accumulation factors 1 and 2, RbcX, and bundle-sheath defective-2 (BSD2). Our structural and functional analysis revealed the role of BSD2 in stabilizing an end-state assembly intermediate of eight RuBisCo large subunits until the small subunits become available. The ability to produce plant RuBisCo recombinantly will facilitate efforts to improve the enzyme through mutagenesis.

    • Organizational Affiliation: 

    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain475Thermosynechococcus vestitus BP-1Mutation(s): 2 
Gene Names: cbbL, rbcL, tll1506
EC: 4.1.1.39
UniProt
Find proteins for Q8DIS5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIS5 
Go to UniProtKB:  Q8DIS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIS5
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ/Hsp40 cysteine-rich domain superfamily protein81Arabidopsis thalianaMutation(s): 0 
Gene Names: F1P2.200, At3g47650
UniProt
Find proteins for Q9SN73 (Arabidopsis thaliana)
Explore Q9SN73 
Go to UniProtKB:  Q9SN73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SN73
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AG [auth D4]
AH [auth H1]
AI [auth J6]
AJ [auth N3]
AK [auth P8]
AG [auth D4],
AH [auth H1],
AI [auth J6],
AJ [auth N3],
AK [auth P8],
AL [auth T5],
BG [auth D4],
BH [auth H1],
BI [auth J6],
BJ [auth N3],
BK [auth P8],
BL [auth T5],
CG [auth D5],
CH [auth H2],
CI [auth J7],
CJ [auth N4],
CK [auth R1],
CL [auth T6],
DG [auth D5],
DH [auth H2],
DI [auth J7],
DJ [auth N4],
DK [auth R1],
DL [auth T6],
EF [auth B1],
EG [auth D6],
EH [auth H3],
EI [auth J8],
EJ [auth N5],
EK [auth R2],
EL [auth T7],
FF [auth B1],
FG [auth D6],
FH [auth H3],
FI [auth J8],
FJ [auth N5],
FK [auth R2],
FL [auth T7],
GF [auth B2],
GG [auth D7],
GH [auth H4],
GI [auth L1],
GJ [auth N6],
GK [auth R3],
GL [auth T8],
HF [auth B2],
HG [auth D7],
HH [auth H4],
HI [auth L1],
HJ [auth N6],
HK [auth R3],
HL [auth T8],
IF [auth B3],
IG [auth D8],
IH [auth H5],
II [auth L2],
IJ [auth N7],
IK [auth R4],
JF [auth B3],
JG [auth D8],
JH [auth H5],
JI [auth L2],
JJ [auth N7],
JK [auth R4],
KF [auth B4],
KG [auth F1],
KH [auth H6],
KI [auth L3],
KJ [auth N8],
KK [auth R5],
LF [auth B4],
LG [auth F1],
LH [auth H6],
LI [auth L3],
LJ [auth N8],
LK [auth R5],
MF [auth B5],
MG [auth F2],
MH [auth H7],
MI [auth L4],
MJ [auth P1],
MK [auth R6],
NF [auth B5],
NG [auth F2],
NH [auth H7],
NI [auth L4],
NJ [auth P1],
NK [auth R6],
OF [auth B6],
OG [auth F3],
OH [auth H8],
OI [auth L5],
OJ [auth P2],
OK [auth R7],
PF [auth B6],
PG [auth F3],
PH [auth H8],
PI [auth L5],
PJ [auth P2],
PK [auth R7],
QF [auth B7],
QG [auth F4],
QH [auth J1],
QI [auth L6],
QJ [auth P3],
QK [auth R8],
RF [auth B7],
RG [auth F4],
RH [auth J1],
RI [auth L6],
RJ [auth P3],
RK [auth R8],
SF [auth B8],
SG [auth F5],
SH [auth J2],
SI [auth L7],
SJ [auth P4],
SK [auth T1],
TF [auth B8],
TG [auth F5],
TH [auth J2],
TI [auth L7],
TJ [auth P4],
TK [auth T1],
UF [auth D1],
UG [auth F6],
UH [auth J3],
UI [auth L8],
UJ [auth P5],
UK [auth T2],
VF [auth D1],
VG [auth F6],
VH [auth J3],
VI [auth L8],
VJ [auth P5],
VK [auth T2],
WF [auth D2],
WG [auth F7],
WH [auth J4],
WI [auth N1],
WJ [auth P6],
WK [auth T3],
XF [auth D2],
XG [auth F7],
XH [auth J4],
XI [auth N1],
XJ [auth P6],
XK [auth T3],
YF [auth D3],
YG [auth F8],
YH [auth J5],
YI [auth N2],
YJ [auth P7],
YK [auth T4],
ZF [auth D3],
ZG [auth F8],
ZH [auth J5],
ZI [auth N2],
ZJ [auth P7],
ZK [auth T4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.918α = 69.4
b = 218.592β = 81.51
c = 310.273γ = 65.5
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Other, Refinement description